Compositions and methods for treating pulmonary hypertension

ABSTRACT

In some aspects, the disclosure relates to GDF/BMP antagonists and methods of using GDF/BMP antagonists to treat, prevent, or reduce the progression rate and/or severity of pulmonary hypertension (PH), particularly treating, preventing or reducing the progression rate and/or severity of one or more PH-associated complications. The disclosure also provides methods of using a GDF/BMP antagonist to treat, prevent, or reduce the progression rate and/or severity of a variety of conditions including, but not limited to, pulmonary vascular remodeling, pulmonary fibrosis, and right ventricular hypertrophy. The disclosure further provides methods of using a GDF/BMP antagonist to reduce right ventricular systolic pressure in a subject in need thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority to U.S. provisionalapplication Ser. No. 62/362,955, filed on Jul. 15, 2016; 62/453,888,filed on Feb. 2, 2017; and 62/510,403, filed on May 24, 2017. Thedisclosures of the foregoing applications are hereby incorporated byreference in their entirety.

BACKGROUND OF THE INVENTION

Pulmonary hypertension (PH) is a disease characterized by high bloodpressure in lung vasculature, including pulmonary arteries, pulmonaryveins, and pulmonary capillaries. In general, PH is defined as a meanpulmonary arterial (PA) pressure ≧25 mm Hg at rest or ≧30 mm Hg withexercise [Hill et al., Respiratory Care 54(7):958-68 (2009)]. The mainPH symptom is difficulty in breathing or shortness of breath, and othersymptoms include fatigue, dizziness, fainting, peripheral edema(swelling in foot, legs or ankles), bluish lips and skin, chest pain,angina pectoris, light-headedness during exercise, non-productive cough,racing pulse and palpitations. PH can be a severe disease causing heartfailure, which is one of the most common causes of death in people whohave pulmonary hypertension. Postoperative pulmonary hypertension maycomplicate many types of surgeries or procedures, and present achallenge associated with a high mortality.

PH may be grouped based on different manifestations of the diseasesharing similarities in pathophysiologic mechanisms, clinicalpresentation, and therapeutic approaches [Simonneau et al., JACC54(1):544-54 (2009)]. Clinical classification of PH was first proposedin 1973, and a recent updated clinical classification was endorsed bythe World Health Organization (WHO) in 2008. According to the updated PHclinical classification, there are five main groups of PH: pulmonaryarterial hypertension (PAH), characterized by a PA wedge pressure ≦15 mmHg; PH owing to a left heart disease (also known as pulmonary venoushypertension or congestive heart failure), characterized by a PA wedgepressure >15 mm Hg; PH owing to lung diseases and/or hypoxia; chronicthromboemboli PH; and PH with unclear or multifactorial etiologies[Simonneau et al., JACC 54(1):544-54 (2009); Hill et al., RespiratoryCare 54(7):958-68 (2009)]. PAH is further classified into idiopathic PAH(IPAH), a sporadic disease in which there is neither a family history ofPAH nor an identified risk factor; heritable PAH; PAH induced by drugsand toxins; PAH associated with connective tissue diseases, HIVinfection, portal hypertension, congenital heart diseases,schistosomiasis, and chronic hemolytic anemia; and persistent PH ofnewborns [Simonneau et al., JACC 54(1):S44-54 (2009)]. Diagnosis ofvarious types of PH requires a series of tests.

In general, PH treatment depends on the cause or classification of thePH. Where PH is caused by a known medicine or medical condition, it isknown as a secondary PH, and its treatment is usually directed at theunderlying disease. Treatment of pulmonary venous hypertension generallyinvolves optimizing left ventricular function by administeringdiuretics, beta blockers, and ACE inhibitors, or repairing or replacinga mitral valve or aortic valve. PAH therapies include pulmonaryvasodilators, digoxin, diuretics, anticoagulants, and oxygen therapy.Pulmonary vasodilators target different pathways, including prostacyclinpathway (e.g., prostacyclins, including intravenous epoprostenol,subcutaneous or intravenous treprostinil, and inhaled iloprost), nitricoxide pathway (e.g., phosphodiesterase-5 inhibitors, includingsildenafil and tadalafil), and endotheline-1 pathway (e.g., endothelinreceptor antagonists, including oral bosentan and oral ambrisentan)[Humbert, M. Am. J. Respir. Crit. Care Med. 179:650-6 (2009); Hill etal., Respiratory Care 54(7):958-68 (2009)]. However, current therapiesprovide no cure for PH, and they do not directly treat the underlingvascular remodeling and muscularization of blood vessels observed inmany PH patients.

Thus, there is a high, unmet need for effective therapies for treatingpulmonary hypertension. Accordingly, it is an object of the presentdisclosure to provide methods for treating, preventing, or reducing theprogression rate and/or severity of PH, particular treating, preventingor reducing the progression rate and/or severity of one or morePH-associated complications.

SUMMARY OF THE INVENTION

In part, the data presented herein demonstrates that GDF/BMP antagonists(inhibitors) can be used to treat pulmonary hypertension. For example,it was shown that a soluble ActRIIA polypeptide and an ALK4:ActRIIBheterodimer can be used, individually, to reduce blood pressure, cardiachypertrophy, and lung weight in a monocrotaline-induced pulmonaryarterial hypertension (PAH) model. Similar positive effects wereobserved for the ActRIIA polypeptide in the Sugen hypoxia PAH model.Histological analysis further revealed that the ActRIIA polypeptide hadsurprising and significant effects on decreasing vascular remodeling andmuscularization of blood vessels in both the monocrotaline-induced andSugen hypoxia models of PAH. Moreover, both the ActRIIA polypeptide andALK4:ActRIIB heterodimer surprisingly had a greater effect onameliorating various complications of PAH compared to sildenafil, whichis a drug approved for the treatment of PAH. Thus, the disclosureestablishes that antagonists of the ActRII (ActRIIA and ActRIIB)signaling pathways may be used to reduce the severity of pulmonaryhypertension. While soluble ActRIIa polypeptides and ALK4:ActRIIBheteromultimers may affect pulmonary hypertension through a mechanismother than ActRIIA/B ligand antagonisms, the disclosure nonethelessdemonstrates that desirable therapeutic agents may be selected on thebasis of ActRII signaling antagonist activity. Therefore, in someembodiments, the disclosure provides methods for using various ActRIIsignaling antagonists for treating hypertension, particularly pulmonaryhypertension, including, for example, antagonists that inhibit one ormore ActRIIA/B ligands [e.g., activin (activin A, activin B, activin AB,activin C, activin AC, activin BC, activin E, activin AE, and/or activinBE), GDF8, GDF11, GDF3, BMP6, BMP15, and BMP10]; antagonists thatinhibit of one or more type I and/or type II receptors (e.g., ActRIIA,ActRIIB, ALK4, ALK7, and ALK5); and antagonists that inhibit one or moredownstream signaling components (e.g., Smad proteins such as Smads 2 and3). As used herein, such signaling antagonists are collectively referredto as “GDF/BMP antagonists” or “GDF/BMP inhibitors”. Accordingly, thedisclosure provides, in part, GDF/BMP antagonist compositions andmethods for treating pulmonary hypertension (e.g., PAH), particularlytreating one or more complications of pulmonary hypertension (e.g.,elevated blood pressure, cardiac hypertrophy, vascular remodeling, andmuscularization of vessels). GDF/BMP antagonists to be used inaccordance with the methods and uses of the disclosure include, forexample, ligand traps (e.g., soluble ActRIIA polypeptides, ActRIIBpolypeptides, ALK4:ActRIIB heterodimers, follistatin polypeptides, andFLRG polypeptides), antibody antagonists, small molecule antagonists,and nucleotide antagonists. Optionally, GDF/BMP antagonists may be usedin combination with one or more supportive therapies and/or additionalactive agents for treating pulmonary hypertension.

In certain aspects, the disclosure relates to methods of treatingpulmonary arterial hypertension comprising administering to a patient inneed thereof an effective amount of an ActRIIA polypeptide. In someembodiments, the ActRIIA polypeptide comprises an amino acid sequencethat is at least 70% (e.g., at least 70%, 75%, 80%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%)identical to an amino acid sequence that begins at any one of aminoacids 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 of SEQ ID NO: 9 and endsat any one of amino acids 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, 134, or 135 of SEQ ID NO: 9. In some embodiments, the ActRIIApolypeptide comprises an amino acid sequence that is at least 70% (e.g.,at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100%) identical to the amino acidsequence of SEQ ID NO: 10. In some embodiments, the ActRIIA polypeptidecomprises an amino acid sequence that is at least 70% (e.g., at least70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100%) identical to the amino acid sequence of SEQID NO: 11. In some embodiments, the ActRIIA polypeptide is a fusionprotein comprising an ActRIIA domain and one or more polypeptide domainsheterologous to ActRIIA. In some embodiments, the ActRIIA polypeptide isa fusion protein comprising an Fc domain of an immunoglobulin. In someembodiments, the Fc domain of the immunoglobulin is an Fc domain of anIgG1 immunoglobulin. In some embodiments, the ActRIIA fusion proteinfurther comprises a linker domain positioned between the ActRIIApolypeptide domain and the one or more heterologous domains (e.g., an Fcimmunoglobulin domain). In some embodiments, the linker domain isselected from the group consisting of: TGGG (SEQ ID NO: 23), TGGGG (SEQID NO: 21), SGGGG (SEQ ID NO: 22), GGGGS (SEQ ID NO: 25), GGG (SEQ IDNO: 19), GGGG (SEQ ID NO: 20), and SGGG (SEQ ID NO: 24). In someembodiments, the ActRIIA polypeptide comprises an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 32. In some embodiments, the ActRIIA polypeptidecomprises the amino acid sequence of SEQ ID NO: 32. In some embodiments,the ActRIIA polypeptide consists of the amino acid sequence of SEQ IDNO: 32. In some embodiments, the ActRIIA polypeptide is part of ahomodimer protein complex. In some embodiments, the ActRIIA polypeptideis glycosylated. In some embodiments, the ActRIIA polypeptide has aglycosylation pattern obtainable by expression in a Chinese hamsterovary cell. In some embodiments, administration of the ActRIIApolypeptide decreases pulmonary arterial pressure in the patient. Insome embodiments, administration of the ActRIIA polypeptide decreasespulmonary arterial pressure in the patient by at least 10% (e.g., 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or atleast 80%). In some embodiments, administration of the ActRIIApolypeptide decreases ventricle hypertrophy in the patient. In someembodiments, administration of the ActRIIA polypeptide decreasesventricle hypertrophy in the patient by at least 10% (e.g., 10%, 15%,20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or at least80%). In some embodiments, administration of the ActRIIA polypeptidedecreases smooth muscle hypertrophy in the patient. In some embodiments,administration of the ActRIIA polypeptide decreases smooth musclehypertrophy in the patient by at least 10% (e.g., 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or at least 80%). Insome embodiments, administration of the ActRIIA polypeptide decreasespulmonary arteriole muscularity in the patient. In some embodiments,administration of the ActRIIA polypeptide decreases pulmonary arteriolemuscularity in the patient by at least 10% (e.g., 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or at least 80%). Insome embodiments, administration of the ActRIIA polypeptide decreasespulmonary vascular resistance in the patient. In some embodiments,administration of the ActRIIA polypeptide decreases pulmonary vascularresistance in the patient by at least 10% (e.g., 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or at least 80%). Insome embodiments, administration of the ActRIIA polypeptide decreasespulmonary vascular resistance in the patient by at least 25-30%. In someembodiments, the patient has pulmonary arterial hypertension and hasFunctional Class II or Class III pulmonary hypertension in accordancewith the World Health Organization's functional classification systemfor pulmonary hypertension. In some embodiments, the patient haspulmonary arterial hypertension that is classified as one or moresubtypes selected from the group consisting of: idiopathic or heritablepulmonary arterial hypertension, drug- and/or toxin-induced pulmonaryhypertension, pulmonary hypertension associated with connective tissuedisease, and pulmonary hypertension associated with congenitalsystemic-to-pulmonary shunts at least 1 year following shunt repair. Insome embodiments, the patient has been treated with one or morevasodilators. In some embodiments, the patient has been treated with oneor more agents selected from the group consisting of: phosphodiesterasetype 5 inhibitors, soluble guanylate cyclase stimulators, prostacyclinreceptor agonist, and endothelin receptor antagonists. In someembodiments, the one or more agents is selected from the groupconsisting of: bosentan, sildenafil, beraprost, macitentan, selexipag,epoprostenol, treprostinil, iloprost, ambrisentan, and tadalafil. Insome embodiments, the method further comprises administration of one ormore vasodilators. In some embodiments, the method further comprisesadministration of one or more agents selected from the group consistingof: phosphodiesterase type 5 inhibitors, soluble guanylate cyclasestimulators, prostacyclin receptor agonist, and endothelin receptorantagonists. In some embodiments, the one or more agents is selectedfrom the group consisting of: bosentan, sildenafil, beraprost,macitentan, selexipag, epoprostenol, treprostinil, iloprost,ambrisentan, and tadalafil. In some embodiments, the patient has a6-minute walk distance from 150 to 400 meters. In some embodiments, themethod increases the patient's 6-minute walk distance by at least 10meters (e.g., at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125,150, 175, 200, 250, 300, or more than 400 meters). In some embodiments,the patient has a hemoglobin level from >8 and <15 g/dl. In someembodiments, the method delays clinical worsening of pulmonary arterialhypertension. In some embodiments, the method delays clinical worseningof pulmonary hypertension in accordance with the World HealthOrganization's functional classification system for pulmonaryhypertension. In some embodiments, the method reduces the risk ofhospitalization for one or more complications associated with pulmonaryarterial hypertension. In some embodiments, the ActRIIA polypeptidesbinds to one or more ligands selected from the group consisting of:activin A, activin B, GDF11, GDF8, BMP10, and BMP6.

In some embodiments, the present disclosure relates to methods oftreating pulmonary hypertension comprising administering to a patient inneed thereof an effective amount of a GDF/BMP antagonist, or combinationof GDF/BMP antagonists. In certain aspects, the disclosure relates tomethods of preventing pulmonary hypertension comprising administering toa patient in need thereof an effective amount of a GDF/BMP antagonist,or combination of GDF/BMP antagonists. In certain aspects, thedisclosure relates to methods of reducing the progression rate ofpulmonary hypertension comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist, or combination ofGDF/BMP antagonists. In some embodiments, the disclosure provides for amethod of treating an interstitial lung disease, comprisingadministering to a patient in need thereof an effective amount of aGDF/BMP antagonist, wherein the GDF/BMP antagonist inhibits one or moreof activin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB,ALK4, ALK5, and ALK7. In some embodiments, the disclosure provides for amethod of treating, preventing, or reducing the progression rate and/orseverity of one or more complications of an interstitial lung disease,comprising administering to a patient in need thereof an effectiveamount of a GDF/BMP antagonist, wherein the GDF/BMP antagonist inhibitsone or more of activin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA,ActRIIB, ALK4, ALK5, and ALK7. In some embodiments, the interstitiallung disease is idiopathic pulmonary fibrosis. In certain aspects, thedisclosure relates to methods of reducing the severity of pulmonaryhypertension comprising administering to a patient in need thereof aneffective amount of a GDF/BMP antagonist, or combination of GDF/BMPantagonists. In certain aspects, the disclosure relates to methods oftreating one or more complications (e.g., smooth muscle and/orendothelial cell proliferation in the pulmonary artery, angiogenesis inthe pulmonary artery, dyspnea, chest pain, pulmonary vascularremodeling, right ventricular hypertrophy, and pulmonary fibrosis) ofpulmonary hypertension comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist, or combination ofGDF/BMP antagonists. In certain aspects, the disclosure relates tomethods of preventing one or more complication of pulmonary hypertension(e.g., smooth muscle and/or endothelial cell proliferation in thepulmonary artery, angiogenesis in the pulmonary artery, dyspnea, chestpain, pulmonary vascular remodeling, right ventricular hypertrophy, andpulmonary fibrosis) comprising administering to a patient in needthereof an effective amount a GDF/BMP antagonist, or combination ofGDF/BMP antagonists. In certain aspects, the disclosure relates tomethods of reducing the progression rate of one or more complication ofpulmonary hypertension (e.g., smooth muscle and/or endothelial cellproliferation in the pulmonary artery, angiogenesis in the pulmonaryartery, dyspnea, chest pain, pulmonary vascular remodeling, rightventricular hypertrophy, and pulmonary fibrosis) comprisingadministering to a patient in need thereof an effective amount a GDF/BMPantagonist, or combination of GDF/BMP antagonists. In certain aspects,the disclosure relates to methods of reducing the severity of one ormore complication of pulmonary hypertension (e.g., smooth muscle and/orendothelial cell proliferation in the pulmonary artery, angiogenesis inthe pulmonary artery, dyspnea, chest pain, pulmonary vascularremodeling, right ventricular hypertrophy, and pulmonary fibrosis)comprising administering to a patient in need thereof an effectiveamount of a GDF/BMP antagonist, or combination of GDF/BMP antagonists.In certain preferred embodiments, methods described herein relate to apatient having pulmonary arterial hypertension. In some embodiments,methods described herein relate to a patient having a resting pulmonaryarterial pressure (PAP) of at least 25 mm Hg (e.g., at least 25, 30, 35,40, 45, or 50 mm Hg). In some embodiments, the methods described hereinreduce PAP in a patient having pulmonary hypertension. For example, themethod may reduce PAP by at least 3 mmHg (e.g., at least 3, 5, 7, 10,12, 15, 20, or 25 mm Hg) in a patient having pulmonary hypertension. Insome embodiments, the methods described herein reduce pulmonary vascularresistance in a patient having pulmonary hypertension. In someembodiments, the methods described herein increase pulmonary capillarywedge pressure in a patient having pulmonary hypertension. In someembodiments, the methods described herein increase left ventricularend-diastolic pressure in a patient having pulmonary hypertension. Insome embodiments, the methods described herein increase (improves)exercise capacity (ability, tolerance) in a patient having pulmonaryhypertension. For example, the method may increase 6-minute walkdistance in a patient having pulmonary hypertension, optionallyincreasing 6-minute walk distance by at least 10 meters (e.g., at least10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more meters). In addition,the method may reduce the patient's Borg dyspnea index (BDI), whichoptionally may be assessed after a 6-minute walk test. In someembodiments, the method reduces the patient's Borg dyspnea index (BDI)by at least 0.5 index points (e.g., at least 0.5, 1, 1.5, 2, 2.5, 3,3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, or 10 indexpoints). In some embodiments, the methods described herein relate to apatient having Class I, Class II, Class III, or Class IV pulmonaryhypertension as recognized by the World Health Organization. In someembodiments, the methods described herein relate to delaying clinicalprogression (worsening) of pulmonary hypertension (e.g., progression asmeasured by the World Health Organization standard). In someembodiments, the method prevents or delays pulmonary hypertension Classprogression (e.g., prevents or delays progression from Class I to ClassII, Class II to Class III, or Class III to Class IV pulmonaryhypertension as recognized by the World Health Organization). In someembodiments, the method promotes or increases pulmonary hypertensionClass regression (e.g., promotes or increases regression from Class IVto Class III, Class III to Class II, or Class II to Class I pulmonaryhypertension as recognized by the World Health Organization). In someembodiments, the patient is further administered one or more supportivetherapies or active agents for treating pulmonary hypertension inaddition to the one or more GDF/BMP antagonist. For example, the patientalso may be administered one or more supportive therapies or activeagents selected from the group consisting of: prostacyclin andderivatives thereof (e.g., epoprostenol, treprostinil, and iloprost);prostacyclin receptor agonists (e.g., selexipag); endothelin receptorantagonists (e.g., thelin, ambrisentan, macitentan, and bosentan);calcium channel blockers (e.g., amlodipine, diltiazem, and nifedipine;anticoagulants (e.g., warfarin); diuretics; oxygen therapy; atrialseptostomy; pulmonary thromboendarterectomy; phosphodiesterase type 5inhibitors (e.g., sildenafil and tadalafil); activators of solubleguanylate cyclase (e.g., cinaciguat and riociguat); ASK-1 inhibitors(e.g., CIIA; SCH79797; GS-4997; MSC2032964A;3H-naphtho[1,2,3-de]quiniline-2,7-diones, NQDI-1;2-thioxo-thiazolidines,5-bromo-3-(4-oxo-2-thioxo-thiazolidine-5-ylidene)-1,3-dihydro-indol-2-one);NF-κantagonists (e.g., dh404, CDDO-epoxide; 2.2-difluoropropionamide;C28 imidazole (CDDO-Im); 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid(CDDO); 3-Acetyloleanolic Acid; 3-Triflouroacetyloleanolic Acid;28-Methyl-3-acetyloleanane; 28-Methyl-3-trifluoroacetyloleanane;28-Methyloxyoleanolic Acid; SZC014; SCZ015; SZC017; PEGylatedderivatives of oleanolic acid; 3-O-(beta-D-glucopyranosyl) oleanolicacid; 3-O-[beta-D-glucopyranosyl-(1- ->3)-beta-D-glucopyranosyl]oleanolic acid; 3-O-[beta-D-glucopyranosyl-(1-->2)-beta-D-glucopyranosyl] oleanolic acid;3-O-[beta-D-glucopyranosyl-(1- ->3)-beta-D-glucopyranosyl] oleanolicacid 28-O-beta-D-glucopyranosyl ester; 3-O-[beta-D-glucopyranosyl-(1-->2)-beta-D-glucopyranosyl] oleanolic acid 28-O-beta-D-glucopyranosylester; 3-O-[a-L-rhamnopyranosyl-(1- ->3)-beta-D-glucuronopyranosyl]oleanolic acid; 3-O-[alpha-L-rhamnopyranosyl-(1-->3)-beta-D-glucuronopyranosyl] oleanolic acid28-O-beta-D-glucopyranosyl ester; 28-O-β-D-glucopyranosyl-oleanolicacid; 3-O-β-D-glucopyranosyl (1→3)-3-D-glucopyranosiduronic acid (CS1);oleanolic acid 3-O-β-D-glucopyranosyl (1→3)-β-D-glucopyranosiduronicacid (CS2); methyl 3,11-dioxoolean-12-en-28-olate (DIOXOL); ZCVI₄-2;Benzyl 3-dehydr-oxy-1,2,5-oxadiazolo[3′,4′:2,3]oleanolate) lung and/orheart transplantation. In some embodiment, the patient may also beadministered a BMP9 polypeptide. In some embodiments the BMP9polypeptide is a mature BMP9 polypeptide. In some embodiments, the BMP9polypeptide comprises a BMP9 prodomain polypeptide. In some embodiments,the BMP9 polypeptide is administered in a pharmaceutical preparation,which optionally may comprise a BMP9 prodomain polypeptide. In such BMP9pharmaceutical preparations comprising a BMP9 prodomain polypeptide, theBMP9 polypeptide may be noncovalently associated with the BMP9 prodomainpolypeptide. In some embodiments, BMP9 pharmaceutical preparations aresubstantially free, or does not comprise, of BMP9 prodomain polypeptide.In some embodiments, the patient may also be administered oleanolic acidor a derivative thereof.

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least GDF11 (e.g., a GDF11 antagonist). Effectson GDF11 inhibition may be determined, for example, using a cell-basedassay including those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at leastGDF11. Ligand binding activity may be determined, for example, using abinding affinity assay including those described herein. In someembodiments, a GDF/BMP antagonist, or combination of antagonists, of thedisclosure binds to at least GDF11 with a K_(D) of at least 1×10⁻⁷ M(e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, atleast 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, variousGDF/BMP antagonists that inhibit GDF11 can be used in accordance withthe methods and uses described herein including, for example, ligandtraps (e.g., ActRII polypeptides, GDF Traps, follistatin polypeptides,FLRG polypeptides, and ALK4:ActRIIB heteromultimers), antibodies, smallmolecules, nucleotide sequences, and combinations thereof. In certainembodiments, a GDF/BMP antagonist, or combination of antagonists, thatinhibits GDF11 may further inhibit one or more of: activin (e.g.,activin A, activin B, activin AB, activin C, activin AC, activin BC,activin E, activin AE, and/or activin BE), GDF8, GDF3, BMP6, BMP15,BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smads (e.g.,Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least GDF8 (e.g., a GDF8 antagonist). Effects onGDF8 inhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at least GDF8.Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least GDF8 with a K_(D) of at least 1×10⁻⁷M (e.g., at least1×10⁻⁸M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹M, or atleast 1×10⁻¹² M). As described herein, various GDF/BMP antagonists thatinhibit GDF8 can be used in accordance with the methods and usesdescribed herein including, for example, ligand traps (e.g., ActRIIpolypeptides, GDF Traps, follistatin polypeptides, FLRG polypeptides,and ALK4:ActRIIB heteromultimers), antibodies, small molecules,nucleotide sequences, and combinations thereof. In certain embodiments,a GDF/BMP antagonist, or combination of antagonists, that inhibits GDF8may further inhibit one or more of: activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE), GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB,ALK4, ALK5, ALK7, and one or more Smads (e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least GDF3 (e.g., a GDF3 antagonist). Effects onGDF3 inhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at least GDF3.Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least GDF3 with a K_(D) of at least 1×10⁻⁷M (e.g., at least1×10⁻⁸M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or atleast 1×10⁻¹²M). As described herein, various GDF/BMP antagonists thatinhibit GDF3 can be used in accordance with the methods and usesdescribed herein including, for example, ligand traps (e.g., ActRIIpolypeptides, GDF Traps, follistatin polypeptides, FLRG polypeptides,and ALK4:ActRIIB heteromultimers), antibodies, small molecules,nucleotide sequences, and combinations thereof. In certain embodiments,a GDF/BMP antagonist, or combination of antagonists, that inhibits GDF3may further inhibit one or more of: activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE), GDF8, GDF11, BMP6, BMP15, BMP10, ActRIIA, ActRIIB,ALK4, ALK5, ALK7, and one or more Smads (e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least BMP6 (e.g., a BMP6 antagonist). Effects onBMP6 inhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at least BMP6.Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least BMP6 with a K_(D) of at least 1×10⁻⁷M (e.g., at least1×10⁻⁸M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M or atleast 1×10⁻¹² M). As described herein, various GDF/BMP antagonists thatinhibit BMP6 can be used in accordance with the methods and usesdescribed herein including, for example, ligand traps (e.g., ActRIIpolypeptides, GDF Traps, follistatin polypeptides, FLRG polypeptides,and ALK4:ActRIIB heteromultimers), antibodies, small molecules,nucleotide sequences, and combinations thereof. In certain embodiments,a GDF/BMP antagonist, or combination of antagonists, that inhibits BMP6may further inhibit one or more of: activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE), GDF8, GDF3, GDF11, BMP15, BMP10, ActRIIA, ActRIIB,ALK4, ALK5, ALK7, and one or more Smads (e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least BMP15 (e.g., a BMP15 antagonist). Effectson BMP15 inhibition may be determined, for example, using a cell-basedassay including those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at leastBMP15. Ligand binding activity may be determined, for example, using abinding affinity assay including those described herein. In someembodiments, a GDF/BMP antagonist, or combination of antagonists, of thedisclosure binds to at least BMP15 with a K_(D) of at least 1×10⁻⁷M(e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various GDF/BMPantagonists that inhibit BMP15 can be used in accordance with themethods and uses described herein including, for example, ligand traps(e.g., ActRII polypeptides, GDF Traps, follistatin polypeptides, FLRGpolypeptides, and ALK4:ActRIIB heteromultimers), antibodies, smallmolecules, nucleotide sequences, and combinations thereof. In certainembodiments, a GDF/BMP antagonist, or combination of antagonists, thatinhibits BMP15 may further inhibit one or more of: activin (e.g.,activin A, activin B, activin AB, activin C, activin AC, activin BC,activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, BMP6,BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smads (e.g.,Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least BMP10 (e.g., a BMP10 antagonist). Effectson BMP10 inhibition may be determined, for example, using a cell-basedassay including those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at leastBMP10. Ligand binding activity may be determined, for example, using abinding affinity assay including those described herein. In someembodiments, a GDF/BMP antagonist, or combination of antagonists, of thedisclosure binds to at least BMP10 with a K_(D) of at least 1×10⁻⁷ M(e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, atleast 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, variousGDF/BMP antagonists that inhibit BMP10 can be used in accordance withthe methods and uses described herein including, for example, ligandtraps (e.g., ActRII polypeptides, GDF Traps, follistatin polypeptides,and FLRG polypeptides, and ALK4:ActRIIB heteromultimers FLRGpolypeptides), antibodies, small molecules, nucleotide sequences, andcombinations thereof. In certain embodiments, a GDF/BMP antagonist, orcombination of antagonists, that inhibits BMP10 may further inhibit oneor more of: activin (e.g., activin A, activin B, activin AB, activin C,activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8,GDF3, GDF11, BMP6, BMP15, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one ormore Smads (e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE) (e.g., an activin antagonist). Effects on activininhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at leastactivin. Ligand binding activity may be determined, for example, using abinding affinity assay including those described herein. In someembodiments, a GDF/BMP antagonist, or combination of antagonists, of thedisclosure binds to at least activin with a K_(D) of at least 1×10⁻⁷M(e.g., at least 1×10⁻⁸M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least1×10⁻¹¹M, or at least 1×10⁻¹² M). As described herein, various GDF/BMPantagonists that inhibit activin can be used in accordance with themethods and uses described herein including, for example, ligand traps(e.g., ActRII polypeptides, GDF Traps, follistatin polypeptides, FLRGpolypeptides, and ALK4:ActRIIB heteromultimers), antibodies, smallmolecules, nucleotide sequences, and combinations thereof. In certainembodiments, a GDF/BMP antagonist, or combination of antagonists, thatinhibits activin may further inhibit one or more of: BMP15 GDF8, GDF3,GDF11, BMP6, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or moreSmads (e.g., Smads 2 and 3). In certain preferred embodiments, a GDF/BMPantagonist, or combination of antagonists, to be used in accordance withmethods and uses described herein is an agent that inhibits at leastactivin B. In some embodiments, a GDF/BMP antagonist, or combination ofantagonists, to be used in accordance with methods and uses describedherein does not substantially bind to activin A (e.g., binds to activinA with a K_(D) higher than 1×10⁻⁷M or has relatively modest binding,e.g., about 1×10⁻⁸M or about 1×10⁻⁹ M) and/or inhibit activin Aactivity. In certain preferred embodiments, a GDF/BMP antagonist, orcombination of antagonists, to be used in accordance with methods anduses described herein is an agent that inhibits at least activin B butdoes not substantially bind to activin A (e.g., binds to activin A witha K_(D) higher than 1×10⁻⁷M or has relatively modest binding, e.g.,about 1×10⁻⁸ M or about 1×10⁻⁹M) and/or inhibit activin A activity.

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least ActRII (e.g., ActRIIA and/or ActRIIB)(e.g., an ActRII antagonist). Effects on ActRII inhibition may bedetermined, for example, using a cell-based assay including thosedescribed herein (e.g., a Smad signaling reporter assay). Therefore, insome embodiments, a GDF/BMP antagonist, or combination of antagonists,of the disclosure may bind to at least ActRII. Ligand binding activitymay be determined, for example, using a binding affinity assay includingthose described herein. In some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure binds to at least ActRIIwith a K_(D) of at least 1×10⁻⁷M (e.g., at least 1×10⁻⁸M, at least1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹M, or at least 1×10⁻¹²M).As described herein, various GDF/BMP antagonists that inhibit ActRII canbe used in accordance with the methods and uses described hereinincluding, for example, ligand traps (e.g., ActRII polypeptides, GDFTraps, follistatin polypeptides, FLRG polypeptides, and ALK4:ActRIIBheteromultimers), antibodies, small molecules, nucleotide sequences, andcombinations thereof. In certain embodiments, a GDF/BMP antagonist, orcombination of antagonists, that inhibits ActRII may further inhibit oneor more of: activin (e.g., activin A, activin B, activin AB, activin C,activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8,GDF3, GDF11, BMP6, BMP15, BMP10, ALK4, ALK5, ALK7, and one or more Smads(e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least ALK4 (e.g., an ALK4 antagonist). Effects onALK4 inhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at least ALK4.Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least ALK4 with a K_(D) of at least 1×10⁻⁷M (e.g., at least1×10⁻⁸M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M or atleast 1×10⁻¹² M). As described herein, various GDF/BMP antagonists thatinhibit ALK4 can be used in accordance with the methods and usesdescribed herein including, for example, ligand traps (e.g., ActRIIpolypeptides, GDF Traps, follistatin polypeptides, FLRG polypeptides,and ALK4:ActRIIB heteromultimers), antibodies, small molecules,nucleotide sequences, and combinations thereof. In certain embodiments,a GDF/BMP antagonist, or combination of antagonists, that inhibits ALK4may further inhibit one or more of: activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE), GDF8, GDF3, GDF11, BMP6, BMP15, BMP10, ActRIIA,ActRIIB, ALK5, ALK7, and one or more Smads (e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least ALK5 (e.g., an ALK5 antagonist). Effects onALK5 inhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonists, orcombination of antagonist, of the disclosure may bind to at least ALK5.Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least ALK5 with a K_(D) of at least 1×10⁻⁷M (e.g., at least1×10⁻⁸M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹M, or atleast 1×10⁻¹² M). As described herein, various GDF/BMP antagonists thatinhibit ALK5 can be used in accordance with the methods and usesdescribed herein including, for example, ligand traps (e.g., ActRIIpolypeptides, GDF Traps, follistatin polypeptides, FLRG polypeptides,and ALK4:ActRIIB heteromultimers), antibodies, small molecules,nucleotide sequences, and combinations thereof. In certain embodiments,a GDF/BMP antagonist, or combination of antagonists, that inhibits ALK5may further inhibit one or more of: activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE), GDF8, GDF3, GDF11, BMP6, BMP15, BMP10, ActRIIA,ActRIIB, ALK7, ALK4, and one or more Smads (e.g., Smads 2 and 3)

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least ALK7 (e.g., an ALK7 antagonist). Effects onALK7 inhibition may be determined, for example, using a cell-based assayincluding those described herein (e.g., a Smad signaling reporterassay). Therefore, in some embodiments, a GDF/BMP antagonist, orcombination of antagonists, of the disclosure may bind to at least ALK7.Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least ALK7 with a K_(D) of at least 1×10⁻⁷M (e.g., at least1×10⁻⁸M, at least 1×10⁻⁹M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or atleast 1×10⁻¹²M). As described herein, various GDF/BMP antagonists thatinhibit ALK7 can be used in accordance with the methods and usesdescribed herein including, for example, ligand traps (e.g., ActRIIpolypeptides, GDF Traps, follistatin polypeptides, FLRG polypeptides,and ALK4:ActRIIB heteromultimers), antibodies, small molecules,nucleotide sequences, and combinations thereof. In certain embodiments,a GDF/BMP antagonist, or combination of antagonists, that inhibits ALK7may further inhibit one or more of: activin (e.g., activin A, activin B,activin AB, activin C, activin AC, activin BC, activin E, activin AE,and/or activin BE), GDF8, GDF3, GDF11, BMP6, BMP15, BMP10, ActRIIA,ActRIIB, ALK5, ALK4, and one or more Smads (e.g., Smads 2 and 3).

In certain aspects, a GDF/BMP antagonist, or combination of antagonists,to be used in accordance with methods and uses described herein is anagent that inhibits at least one or more Smad proteins (e.g., Smads 2and 3). Effects on Smad inhibition may be determined, for example, usinga cell-based assay including those described herein (e.g., a Smadsignaling reporter assay). Therefore, in some embodiments, a GDF/BMPantagonist, or combination of antagonists, of the disclosure may bind toat least one or more one or more Smad proteins (e.g., Smads 2 and 3).Ligand binding activity may be determined, for example, using a bindingaffinity assay including those described herein. In some embodiments, aGDF/BMP antagonist, or combination of antagonists, of the disclosurebinds to at least one or more Smad proteins (e.g., Smads 2 and 3) with aK_(D) of at least 1×10⁻⁷M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹M, atleast 1×10⁻¹⁰ M, at least 1×10⁻¹¹M, or at least 1×10⁻¹²M). As describedherein, various GDF/BMP antagonists that inhibit one or more Smadproteins (e.g., Smads 2 and 3) can be used in accordance with themethods and uses described herein including, for example, ligand traps(e.g., ActRII polypeptides, GDF Traps, follistatin polypeptides, FLRGpolypeptides, and ALK4:ActRIIB heteromultimers), antibodies, smallmolecules, nucleotide sequences, and combinations thereof. In certainembodiments, a GDF/BMP antagonist, or combination of antagonists, thatinhibits one or more Smad proteins (e.g., Smads 2 and 3) may furtherinhibit one or more of: activin (e.g., activin A, activin B, activin AB,activin C, activin AC, activin BC, activin E, activin AE, and/or activinBE), GDF8, GDF3, GDF11, BMP6, BMP15, BMP10, ActRIIA, ActRIIB, ALK5, andALK4.

In certain aspects, a GDF/BMP antagonist to be used in accordance withmethods and uses described herein is an ActRII polypeptide. The term“ActRII polypeptide” collectively refers to naturally occurring ActRIIAand ActRIIB polypeptides as well as truncations and variants thereofsuch as those described herein (e.g., GDF trap polypeptides). PreferablyActRII polypeptides comprise, consist essentially of, or consist of aligand-binding domain of an ActRII polypeptide or modified (variant)form thereof. For example, in some embodiments, an ActRIIA polypeptidecomprises, consists essentially of, or consists of an ActRIIAligand-binding domain of an ActRIIA polypeptide, for example, a portionof the ActRIIA extracellular domain. Similarly, an ActRIIB polypeptidemay comprise, consist essentially of, or consist of an ActRIIBligand-binding domain of an ActRIIB polypeptide, for example, a portionof the ActRIIB extracellular domain. Preferably, ActRII polypeptides tobe used in accordance with the methods described herein are solublepolypeptides.

In certain aspects, the disclosure relates compositions comprising anActRIIA polypeptide and uses thereof. For example, in some embodiments,an ActRIIA polypeptide of the disclosure comprises an amino acidsequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of aminoacids 30-110 of SEQ ID NO: 9. In some embodiments, an ActRIIApolypeptides of the discloses comprises an amino acid sequence that isat least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIAbeginning at a residue corresponding to any one of amino acids 21-30(e.g., beginning at any one of amino acids 21, 22, 23, 24, 25, 26, 27,28, 29, or 30) of SEQ ID NO: 9 and ending at a position corresponding toany one amino acids 110-135 (e.g., ending at any one of amino acids 110,111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,125, 126, 127, 128, 129, 130, 131, 132, 133, 134, or 135) of SEQ ID NO:9. In other embodiments, an ActRIIA polypeptide may comprise an aminoacid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 9. In other embodiments, an ActRIIA polypeptidemay comprise of an amino acid sequence that is at least 70%, 75%, 80%,85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identicalto the amino acid sequence of SEQ ID NO: 10. In even other embodiments,an ActRIIA polypeptide may comprise of an amino acid sequence that is atleast 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to the amino acid sequence of SEQ ID NO: 11. Instill other embodiments, an ActRIIA polypeptide may comprise an aminoacid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 32. In still even other embodiments, an ActRIIApolypeptide may comprise, consist essentially of, or consist of an aminoacid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 36. In still even other embodiments, an ActRIIApolypeptide may comprise, consist essentially of, or consist of an aminoacid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 39.

In other aspects, the disclosure relates compositions comprising anActRIIB polypeptide and uses thereof. For example, in some embodiments,an ActRIIB polypeptide of the disclosure comprises an amino acidsequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of aminoacids 29-109 of SEQ ID NO: 1. In some embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the sequence of amino acids 29-109 of SEQ ID NO: 1, whereinthe ActRIIB polypeptide comprises an acidic amino acid [naturallyoccurring (E or D) or artificial acidic amino acid] at position 79 withrespect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe sequence of amino acids 25-131 of SEQ ID NO: 1. In some embodiments,an ActRIIB polypeptide may comprise an amino acid sequence that is atleast 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to the sequence of amino acids 25-131 of SEQ IDNO: 1, wherein the ActRIIB polypeptide comprises an acidic amino acid atposition 79 with respect to SEQ ID NO: 1. In some embodiments, anActRIIB polypeptide may comprise an amino acid sequence that is at least70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or100% identical to a sequence starting at a residue corresponding to anyone of amino acids 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 of SEQ IDNO: 1 and ending at a residue corresponding to any one of amino acids109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134 of SEQ IDNO: 1. In other embodiments, an ActRIIB polypeptide may comprise anamino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequencestarting at a residue corresponding to any one of amino acids 20, 21,22, 23, 24, 25, 26, 27, 28, or 29 of SEQ ID NO: 1 and ending at aresidue corresponding to any one of amino acids 109, 110, 111, 112, 113,114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127,128, 129, 130, 131, 132, 133, or 134 of SEQ ID NO: 1, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 1. In some embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 1, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 1. In even other embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 2. In otherembodiments, an ActRIIB polypeptide may comprise an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ IDNO: 2, wherein the ActRIIB polypeptide comprises an acidic amino acid atposition 79 with respect to SEQ ID NO: 1. In still other embodiments, anActRIIB polypeptide may comprise an amino acid sequence that is at least70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or100% identical to the amino acid sequence of SEQ ID NO: 3. In other, anActRIIB polypeptide may comprise an amino acid sequence that is at least70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or100% identical to the amino acid sequence of SEQ ID NO: 3, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 4. In some embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 4, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 4. In other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 5. In some embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 5, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 5. In other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 6. In some embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 6, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 6. In still even other embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 40. In still evenother embodiments, an ActRIIB polypeptide may comprise an amino acidsequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence ofSEQ ID NO: 42. In still even other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 45. In still even otherembodiments, an ActRIIB polypeptide may comprise an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ IDNO: 46. In some embodiments, an ActRIIB polypeptide may comprise anamino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 46, wherein the ActRIIB polypeptide comprises anacidic amino acid at position 79 with respect to SEQ ID NO: 1. In stilleven other embodiments, an ActRIIB polypeptide may comprise an aminoacid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 47. In some embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 47, wherein the ActRIIBpolypeptide comprises an acidic amino acid at position 79 with respectto SEQ ID NO: 1. In still even other embodiments, an ActRIIB polypeptidemay comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 48. In some embodiments, anActRIIB polypeptide may comprise an amino acid sequence that is at least70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or100% identical to the amino acid sequence of SEQ ID NO: 48, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 1. In still even other embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 69. In still evenother embodiments, an ActRIIB polypeptide may comprise an amino acidsequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence ofSEQ ID NO: 74. In some embodiments, an ActRIIB polypeptide may comprisean amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the aminoacid sequence of SEQ ID NO: 74, wherein the ActRIIB polypeptidecomprises an acidic amino acid at position 79 with respect to SEQ IDNO: 1. In still even other embodiments, an ActRIIB polypeptide maycomprise an amino acid sequence that is at least 70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 77. In some embodiments, anActRIIB polypeptide may comprise an amino acid sequence that is at least70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or100% identical to the amino acid sequence of SEQ ID NO: 77, wherein theActRIIB polypeptide comprises an acidic amino acid at position 79 withrespect to SEQ ID NO: 1. In still even other embodiments, an ActRIIBpolypeptide may comprise an amino acid sequence that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 78. In someembodiments, an ActRIIB polypeptide may comprise an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ IDNO: 78, wherein the ActRIIB polypeptide comprises an acidic amino acidat position 79 with respect to SEQ ID NO: 1. In still even otherembodiments, an ActRIIB polypeptide may comprise an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ IDNO: 79. In some embodiments, an ActRIIB polypeptide may comprise anamino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO: 79, wherein the ActRIIB polypeptide comprises anacidic amino acid at position 79 with respect to SEQ ID NO: 1. Incertain embodiments, ActRIIB polypeptides to be used in accordance withthe methods and uses described herein do not comprise an acidic aminoacid at the position corresponding to L79 of SEQ ID NO: 1.

As described herein, ActRII polypeptides, ALK4 polypeptides and variantsthereof (GDF traps) may be homomultimers, for example, homodimer,homotrimers, homotetramers, homopentamers, and higher order homomultimercomplexes. In certain preferred embodiments, ActRII polypeptides andvariants thereof are homodimers. In certain embodiments, ActRIIpolypeptide dimers described herein comprise an first ActRII polypeptidecovalently, or non-covalently, associated with an second ActRIIpolypeptide wherein the first polypeptide comprises an ActRII domain andan amino acid sequence of a first member (or second member) of aninteraction pair (e.g., a constant domain of an immunoglobulin) and thesecond polypeptide comprises an ActRII polypeptide and an amino acidsequence of a second member (or first member) of the interaction pair.

In certain aspects, a GDF/BMP antagonist to be used in accordance withmethods and uses described herein is an ALK4:ActRIIB heteromultimer. Asdescribed herein, it has been discovered that an ALK4:ActRIIBheterodimer protein complex has a different ligand-bindingprofile/selectivity compared to corresponding ActRIIB and ALK4homodimers. In particular, ALK4:ActRIIB heterodimer displays enhancedbinding to activin B compared to either homodimer, retains strongbinding to activin A, GDF8, and GDF11 as observed with ActRIIBhomodimer, and exhibits substantially reduced binding to BMP9, BMP10,and GDF3. In particular, BMP9 displays low to no observable affinity forALK4:ActRIIB heterodimer, whereas this ligand binds strongly to ActRIIBhomodimer. Like ActRIIB homodimer, ALK4:ActRIIB heterodimer retainsintermediate-level binding to BMP6. See FIG. 19. These results thereforedemonstrate that ALK4:ActRIIB heterodimers are a more selectiveantagonists (inhibitors) of activin A, activin B, GDF8, and GDF11compared to ActRIIB homodimers. Accordingly, an ALK4:ActRIIB heterodimerwill be more useful than an ActRIIB homodimer in certain applicationswhere such selective antagonism is advantageous. Examples includetherapeutic applications where it is desirable to retain antagonism ofone or more of activin (e.g., activin A, activin B, activin AB, activinAC), GDF8, and GDF11 but minimize antagonism of one or more of BMP9,BMP10, and GDF3. Moreover, an ALK4:ActRIIB heterodimer has been showntreat PAH in patient. While not wishing to be bound to a particularmechanisms of action, it is expected that ALK4:ActRIIB heteromultimers,as well as variants thereof, that bind to at least one or more ofactivin (e.g., activin A, activin B, activin AB, and activin AC), GDF8,and/or GDF11 will be useful agents for promoting beneficial effects inPAH patients.

Therefore, the present disclosure provides heteromultimer complexes(heteromultimers) comprising at least one ALK4 polypeptide and at leastone ActRIIB polypeptide (ALK4:ActRIIB heteromultimers) as well as usesthereof. Preferably, ALK4 polypeptides comprise a ligand-binding domainof an ALK4 receptor, for example, a portion of the ALK4 extracellulardomain. Similarly, ActRIIB polypeptides generally comprise aligand-binding domain of an ActRIIB receptor, for example, a portion ofthe ActRIIB extracellular domain. Preferably, such ALK4 and ActRIIBpolypeptides, as well as resultant heteromultimers thereof, are soluble.

In certain aspects, an ALK4:ActRIIB heteromultimer comprises an aminoacid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical toamino acids 34-101 of SEQ ID NO: 100. In other embodiments, ALK4:ActRIIBheteromultimers comprises an ALK4 amino acid sequence that is at least70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 101. In otherembodiments, ALK4:ActRIIB heteromultimers comprises an ALK4 amino acidsequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ IDNO: 105. In other embodiments, ALK4:ActRIIB heteromultimers comprises anALK4 amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to SEQ ID NO: 122. In other embodiments, ALK4:ActRIIBheteromultimers comprise an ALK4 amino acid sequence that is at least70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 124. In otherembodiments, ALK4:ActRIIB heteromultimers comprise an ALK4 amino acidsequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ IDNO: 116. In still other embodiments, ALK4:ActRIIB heteromultimerscomprises an ALK4 amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to SEQ ID NO: 117. In other embodiments,ALK4:ActRIIB heteromultimers comprise an ALK4 amino acid sequence thatis at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 111. Instill other embodiments, ALK4:ActRIIB heteromultimers comprises an ALK4amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identicalto SEQ ID NO: 113.

In certain aspects, an ALK4:ActRIIB heteromultimer comprises an ActRIIBamino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identicalto amino acids 29-109 of SEQ ID NO: 1. In other embodiments,ALK4:ActRIIB heteromultimers comprises an ActRIIB amino acid sequencethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 2. Inother embodiments, ALK4:ActRIIB heteromultimers comprise an ActRIIBamino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identicalto SEQ ID NO: 3. In other embodiments, ALK4:ActRIIB heteromultimerscomprise an ActRIIB amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to SEQ ID NO: 5. In other embodiments,ALK4:ActRIIB heteromultimers comprises an ActRIIB amino acid sequencethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 6. Inother embodiments, ALK4:ActRIIB heteromultimers comprise an ActRIIBamino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identicalto SEQ ID NO: 118. In still even other embodiments, ALK4:ActRIIBheteromultimers comprises an ActRIIB amino acid sequence that is atleast 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 120 In otherembodiments, ALK4:ActRIIB heteromultimers comprise an ActRIIB amino acidsequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ IDNO: 114. In other embodiments, ALK4:ActRIIB heteromultimers may comprisean ActRIIB amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to SEQ ID NO: 115. In other embodiments, ALK4:ActRIIBheteromultimers comprise an ActRIIB amino acid sequence that is at least70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 108. In otherembodiments, ALK4:ActRIIB heteromultimers may comprise an ActRIIB aminoacid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical toSEQ ID NO: 110. In certain preferred embodiments, ALK4:ActRIIBheteromultimers do not comprise an ActRIIB polypeptide comprising anacidic amino acid (e.g., an E or D) at the position corresponding to L79of SEQ ID NO: 1.

As described herein, ALK4:ActRIIB heteromultimer structures include, forexample, heterodimers, heterotrimers, heterotetramers, heteropentamers,and higher order heteromultimer complexes. See, e.g., FIGS. 21-23. Incertain preferred embodiments, ALK4:ActRIIB heteromultimers areheterodimers. In certain aspects, ALK4 and/or ActRIIB polypeptides maybe fusion proteins.

In certain aspects, ActRII polypeptides, ALK4 polypeptides, includingvariants thereof (e.g., GDF traps), may be fusion proteins. For example,in some embodiments, an ActRII (or ALK4) polypeptide may be a fusionprotein comprising an ActRII (or ALK4) polypeptide domain and one ormore heterologous (non-ActRII) polypeptide domains. In some embodiments,an ActRII (or ALK4) polypeptide may be a fusion protein that has, as onedomain, an amino acid sequence derived from an ActRII (or ALK4)polypeptide (e.g., a ligand-binding domain of an ActRII (or ALK4)receptor or a variant thereof) and one or more heterologous domains thatprovide a desirable property, such as improved pharmacokinetics, easierpurification, targeting to particular tissues, etc. For example, adomain of a fusion protein may enhance one or more of in vivo stability,in vivo half-life, uptake/administration, tissue localization ordistribution, formation of protein complexes, multimerization of thefusion protein, and/or purification. Optionally, an ActRII (or ALK4)polypeptide domain of a fusion protein is connected directly (fused) toone or more heterologous polypeptide domains or an intervening sequence,such as a linker, may be positioned between the amino acid sequence ofthe ActRII (or ALK4) polypeptide and the amino acid sequence of the oneor more heterologous domains. In certain embodiments, an ActRII (orALK4) fusion protein comprises a relatively unstructured linkerpositioned between the heterologous domain and the ActRII (or ALK4)domain. This unstructured linker may correspond to the roughly 15 aminoacid unstructured region at the C-terminal end of the extracellulardomain of ActRII (or ALK4), or it may be an artificial sequence ofbetween 3 and 15, 20, 30, 50 or more amino acids that are relativelyfree of secondary structure. A linker may be rich in glycine and/orproline residues and may, for example, contain repeating sequences ofthreonine/serine and glycines. Examples of linkers include, but are notlimited to, the sequences TGGG (SEQ ID NO: 23), SGGG (SEQ ID NO: 24),TGGGG (SEQ ID NO: 21), SGGGG (SEQ ID NO: 22), GGGGS (SEQ ID NO: 25),GGGG (SEQ ID NO: 20), and GGG (SEQ ID NO: 19). In some embodiments,ActRII (or ALK4) fusion proteins may comprise a constant domain of animmunoglobulin, including, for example, the Fc portion of animmunoglobulin. For example, an amino acid sequence that is derived froman Fc domain of an IgG (IgG1, IgG2, IgG3, or IgG4), IgA (IgA1 or IgA2),IgE, or IgM immunoglobulin. For example, an Fc portion of animmunoglobulin domain may comprise, consist essentially of, or consistof an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to any one ofSEQ ID NOs: 14-18. Such immunoglobulin domains may comprise one or moreamino acid modifications (e.g., deletions, additions, and/orsubstitutions) that confer an altered Fc activity, e.g., decrease of oneor more Fc effector functions. In some embodiment, an ActRII (or ALK4)fusion protein comprises an amino acid sequence as set forth in theformula A-B-C. For example, the B portion is an N- and C-terminallytruncated ActRII (or ALK4) polypeptide, e.g., as described herein. The Aand C portions may be independently zero, one, or more than one aminoacids, and both A and C portions are heterologous to B. The A and/or Cportions may be attached to the B portion via a linker sequence. Incertain embodiments, an ActRII (or ALK4) fusion protein comprises aleader sequence. The leader sequence may be a native ActRII (or ALK4)leader sequence or a heterologous leader sequence. In certainembodiments, the leader sequence is a tissue plasminogen activator (TPA)leader sequence (e.g., SEQ ID NO: 34).

An ActRII polypeptide or ALK4 polypeptide, including variants thereof,may comprise a purification subsequence, such as an epitope tag, a FLAGtag, a polyhistidine sequence, and a GST fusion. Optionally, an ActRIIpolypeptide or ALK4 polypeptide comprises one or more modified aminoacid residues selected from: a glycosylated amino acid, a PEGylatedamino acid, a farnesylated amino acid, an acetylated amino acid, abiotinylated amino acid, and/or an amino acid conjugated to a lipidmoiety. ActRII polypeptides and ALK4 polypeptides may comprise at leastone N-linked sugar, and may include two, three or more N-linked sugars.Such polypeptides may also comprise O-linked sugars. In general, it ispreferable that ActRII and ALK4 polypeptides be expressed in a mammaliancell line that mediates suitably natural glycosylation of thepolypeptide so as to diminish the likelihood of an unfavorable immuneresponse in a patient. ActRII and ALK4 polypeptides may be produced in avariety of cell lines that glycosylate the protein in a manner that issuitable for patient use, including engineered insect or yeast cells,and mammalian cells such as COS cells, CHO cells, HEK cells and NSOcells. In some embodiments, an ActRII or ALK4 polypeptide isglycosylated and has a glycosylation pattern obtainable from a Chinesehamster ovary cell line. In some embodiments, ActRII or ALK4polypeptides of the disclosure exhibit a serum half-life of at least 4,6, 12, 24, 36, 48, or 72 hours in a mammal (e.g., a mouse or a human).Optionally, ActRII or ALK4 polypeptides may exhibit a serum half-life ofat least 6, 8, 10, 12, 14, 20, 25, or 30 days in a mammal (e.g., a mouseor a human).

In certain aspects, the disclosure provides pharmaceutical preparationscomprising one or more GDF/BMP antagonists of the present disclosure anda pharmaceutically acceptable carrier. A pharmaceutical preparation mayalso comprise one or more additional active agents such as a compoundthat is used to treat pulmonary hypertension, particularly treating orpreventing one or more complications of pulmonary hypertension (e.g.,smooth muscle and/or endothelial cell proliferation in the pulmonaryartery, angiogenesis in the pulmonary artery, dyspnea, chest pain,pulmonary vascular remodeling, right ventricular hypertrophy, andpulmonary fibrosis) including, for example, vasodilators such asprostacyclin, epoprostenol, and sildenafil; endothelin receptorantagonists such as bosentan; calcium channel blockers such asamlodipine, diltiazem, and nifedipine; anticoagulants such as warfarin;diuretics; BMP9 polypeptides; BMP10 polypeptides; bardoxolone methyl;and oleanolic acid. In general pharmaceutical preparation willpreferably be pyrogen-free (meaning pyrogen free to the extent requiredby regulations governing the quality of products for therapeutic use).

In certain instances, when administering an GDF/BMP antagonist, orcombination of antagonists, of the disclosure to disorders or conditionsdescribed herein, it may be desirable to monitor the effects on redblood cells during administration of the GDF/BMP antagonist, or todetermine or adjust the dosing of the GDF/BMP antagonist, in order toreduce undesired effects on red blood cells. For example, increases inred blood cell levels, hemoglobin levels, or hematocrit levels may causeundesirable increases in blood pressure.

In certain aspects, a GDF/BMP antagonist to be used in accordance withmethods and uses of the disclosure is an antibody, or combination ofantibodies. In some embodiments, the antibody binds to at least ActRII(ActRIIA and/or ActRIIB) In certain embodiments, an antibody that bindsto ActRII inhibits ActRII signaling, optionally as measured in acell-based assay such as those described herein. In certain embodiments,an antibody that binds to ActRII inhibits one or more GDF/BMP ligands,type I receptors, or co-receptors from binding to ActRII. In certainembodiments an antibody that binds to ActRII inhibits one or moreGDF/BMP ligands from binding to ActRII selected from the groupconsisting of: activin (e.g., activin A, activin B, activin C, activinAB, activin AC, activin BC, activin E, activin AE, and activin BE),GDF8, GDF11, BMP6, BMP15, BMP10, and GDF3. In some embodiments, theantibody binds to at least ALK4. In certain embodiments, an antibodythat binds to ALK4 inhibits ALK4 signaling, optionally as measured in acell-based assay such as those described herein. In certain embodiments,an antibody that binds to ALK4 inhibits one or more GDF/BMP ligands,type II receptors, or co-receptors from binding to ALK4. In certainembodiments an antibody that binds to ALK4 inhibits one or more GDF/BMPligands from binding to ALK4 selected from the group consisting of:activin (e.g., activin A, activin B, activin C, activin AB, activin AC,activin BC, activin E, activin AE, and activin BE), GDF8, GDF11, BMP6,BMP15, BMP10, and GDF3. In some embodiments, the antibody binds to atleast ALK5. In certain embodiments, an antibody that binds to ALK5inhibits ALK5 signaling, optionally as measured in a cell-based assaysuch as those described herein. In certain embodiments, an antibody thatbinds to ALK5 inhibits one or more GDF/BMP ligands, type II receptors,or co-receptors from binding to ALK5. In certain embodiments an antibodythat binds to ALK5 inhibits one or more GDF/BMP ligands from binding toALK5 selected from the group consisting of: activin (e.g., activin A,activin B, activin C, activin AB, activin AC, activin BC, activin E,activin AE, and activin BE), GDF8, GDF11, BMP6, BMP15, BMP10, and GDF3.In some embodiments, the antibody binds to at least

ALK7. In certain embodiments, an antibody that binds to ALK7 inhibitsALK7 signaling, optionally as measured in a cell-based assay such asthose described herein. In certain embodiments, an antibody that bindsto ALK7 inhibits one or more GDF/BMP ligands, type II receptors, orco-receptors from binding to ALK7. In certain embodiments an antibodythat binds to ALK7 inhibits one or more GDF/BMP ligands from binding toALK7 selected from the group consisting of: activin (e.g., activin A,activin B, activin C, activin AB, activin AC, activin BC, activin E,activin AE, and activin BE), GDF8, GDF11, BMP6, BMP15, BMP10, and GDF3.In some embodiments, the antibody binds to at least GDF11. In certainembodiments, an antibody that binds to GDF11 inhibits ActRII signaling,optionally as measured in a cell-based assay such as those describedherein. In certain embodiments, an antibody that binds to GDF11 inhibitsGDF11-ActRII binding and/or GDF11-ALK binding (e.g., GDF11-ALK4,GDF11-ALK5, and/or GDF11-ALK7 binding). In some embodiments, theantibody binds to at least GDF8. In certain embodiments, an antibodythat binds to GDF8 inhibits ActRII signaling, optionally as measured ina cell-based assay such as those described herein. In certainembodiments, an antibody that binds to GDF8 inhibits GDF8-ActRII bindingand/or GDF8-ALK binding (e.g., GDF8-ALK4, GDF8-ALK5, and/or GDF8-ALK7binding). In some embodiments, the antibody binds to at least BMP6. Incertain embodiments, an antibody that binds to BMP6 inhibits ActRIIsignaling, optionally as measured in a cell-based assay such as thosedescribed herein. In certain embodiments, an antibody that binds to BMP6inhibits BMP6-ActRII binding and/or BMP6-ALK binding (e.g., BMP6-ALK4,BMP6-ALK5, and/or BMP6-ALK7 binding). In some embodiments, the antibodybinds to at least BMP15. In certain embodiments, an antibody that bindsto BMP15 inhibits ActRII signaling, optionally as measured in acell-based assay such as those described herein. In certain embodiments,an antibody that binds to BMP15 inhibits BMP15-ActRII binding and/orBMP15-ALK binding (e.g., BMP15-ALK4, BMP15-ALK5, and/or BMP15-ALK7binding). In some embodiments, the antibody binds to at least GDF3. Incertain embodiments, an antibody that binds to GDF3 inhibits ActRIIsignaling, optionally as measured in a cell-based assay such as thosedescribed herein. In certain embodiments, an antibody that binds to GDF3inhibits GDF3-ActRII binding and/or GDF3-ALK binding (e.g., GDF3-ALK4,GDF3-ALK5, and/or GDF3-ALK7 binding). In some embodiments, the antibodybinds to at least BMP10. In certain embodiments, an antibody that bindsto BMP10 inhibits ActRII signaling, optionally as measured in acell-based assay such as those described herein. In certain embodiments,an antibody that binds to BMP10 inhibits BMP10-ActRII binding and/orBMP10-ALK binding (e.g., BMP10-ALK4, BMP10-ALK5, and/or BMP10-ALK7binding). In some embodiments, the antibody binds to activin (e.g.activin A, activin B, activin C, activin AB, activin AC, activin BC,activin E, activin AE, and activin BE). In certain embodiments, anantibody that binds to activin (e.g. activin A, activin B, activin C,activin AB, activin AC, activin BC, activin E, activin AE, and activinBE) inhibits ActRII signaling, optionally as measured in a cell-basedassay such as those described herein. In certain embodiments, anantibody that binds to activin (e.g. activin A, activin B, activin C,activin AB, activin AC, activin BC, activin E, activin AE, and activinBE) inhibits activin-ActRII binding and/or activin-ALK binding (e.g.,activin-ALK4, activin-ALK5, and/or activin-ALK7 binding). In someembodiments, the antibody binds to activin B. In certain embodiments, anantibody that binds to activin B inhibits ActRII signaling, optionallyas measured in a cell-based assay such as those described herein. Incertain embodiments, an antibody that binds to activin B inhibitsactivin B-ActRII binding and/or activin B-ALK binding (e.g., activinB-ALK4, activin B-ALK5, and/or activin B-ALK7 binding). In someembodiments, the antibody is a multispecific antibody, or combination ofmultispecific antibodies that binds to one or more of ActRIIB, ActRIIA,ALK4, ALK5, ALK7, GDF11, GDF8, activin, BMP6, GDF3, BMP10, and BMP15. Incertain aspects the multispecific antibody, or a combination ofmultispecific antibodies, inhibits signaling in a cell-based assay ofone or more of: ActRIIB, GDF11, GDF8, activin, BMP6, GDF3, BMP10 andBMP15. In some embodiments, antibody is a chimeric antibody, a humanizedantibody, or a human antibody. In some embodiments, the antibody is asingle-chain antibody, an F(ab′)₂ fragment, a single-chain diabody, atandem single-chain Fv fragment, a tandem single-chain diabody, a or afusion protein comprising a single-chain diabody and at least a portionof an immunoglobulin heavy-chain constant region.

In certain aspects, the GDF/BMP antagonist is a small molecule inhibitoror combination of small molecule inhibitors. In some embodiments, thesmall molecule inhibitor is an inhibitor of at least ActRII (e.g.,ActRIIA and/or ActRIIB) In some embodiments, the small moleculeinhibitor is an inhibitor of at least ALK4. In some embodiments, thesmall molecule inhibitor is an inhibitor of at least ALK5. In someembodiments, the small molecule inhibitor is an inhibitor of at leastALK7. In some embodiments, the small molecule inhibitor is an inhibitorof at least GDF11. In some embodiments, the small molecule inhibitor isan inhibitor of at least GDF8. In some embodiments, the small moleculeinhibitor is an inhibitor of at least BMP6. In some embodiments, thesmall molecule inhibitor is an inhibitor of at least BMP15. In someembodiments, the small molecule inhibitor is an inhibitor of at leastBMP10. In some embodiments, the small molecule inhibitor is an inhibitorof at least GDF3. In some embodiments, the small molecule inhibitor isan inhibitor of at least activin (e.g. activin A, activin B, activin C,activin AB, activin AC, activin BC, activin E, activin AE, and activinBE). In some embodiments, the small molecule inhibitor is an inhibitorof at least activin B. In some embodiments, the small molecule inhibitoris an inhibitor of at least one or more Smad proteins (e.g., Smads 2 and3).

In certain aspects, the GDF/BMP antagonist is a nucleic acid inhibitoror combination of nucleic acid inhibitors. In some embodiments, thenucleic acid inhibitor is an inhibitor of at least ActRII (e.g., ActRIIAand/or ActRIIB) In some embodiments, the nucleic acid inhibitor is aninhibitor of at least ALK4. In some embodiments, the nucleic acidinhibitor is an inhibitor of at least ALK5. In some embodiments, thenucleic acid inhibitor is an inhibitor of at least ALK7. In someembodiments, the nucleic acid inhibitor is an inhibitor of at leastGDF11. In some embodiments, the nucleic acid inhibitor is an inhibitorof at least GDF8. In some embodiments, the nucleic acid inhibitor is aninhibitor of at least BMP6. In some embodiments, the nucleic acidinhibitor is an inhibitor of at least BMP15. In some embodiments, thenucleic acid inhibitor is an inhibitor of at least BMP10. In someembodiments, the nucleic acid inhibitor is an inhibitor of at leastGDF3. In some embodiments, the nucleic acid inhibitor is an inhibitor ofat least activin (e.g. activin A, activin B, activin C, activin AB,activin AC, activin BC, activin E, activin AE, and activin BE). In someembodiments, the nucleic acid inhibitor is an inhibitor of at leastactivin B. In some embodiments, the nucleic acid inhibitor is aninhibitor of at least one or more Smads (e.g., Smads 2 and 3).

In certain aspects, the GDF/BMP antagonist is a follistatin polypeptide.In some embodiments, the follistatin polypeptide comprises an amino acidsequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence ofSEQ ID NO: 26. In some embodiments, the follistatin polypeptidecomprises an amino acid sequence that is at least 70%, 75% 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 27. In some embodiments, thefollistatin polypeptide comprises an amino acid sequence that is atleast 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to the amino acid sequence of SEQ ID NO: 28. Insome embodiments, the follistatin polypeptide comprises an amino acidsequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence ofSEQ ID NO: 29. In some embodiments, the follistatin polypeptidecomprises an amino acid sequence that is at least 70%, 75% 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical tothe amino acid sequence of SEQ ID NO: 30.

In certain aspects, the GDF/BMP antagonist is a FLRG polypeptide. Insome embodiments, the FLRG polypeptide comprises an amino acid sequencethat is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ IDNO: 31.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor.

FIG. 1 shows an alignment of extracellular domains of human ActRIIB (SEQID NO: 2) and human ActRIIA (SEQ ID NO: 10) with the residues that arededuced herein, based on composite analysis of multiple ActRIIB andActRIIA crystal structures, to directly contact ligand indicated withboxes.

FIG. 2 shows a multiple sequence alignment of various vertebrate ActRIIBproteins (SEQ ID NOs: 53-58) and human ActRIIA (SEQ ID NO: 59) as wellas a consensus ActRII sequence derived from the alignment (SEQ ID NO:60).

FIG. 3 shows a multiple sequence alignment of various vertebrate ActRIIAproteins and human ActRIIA (SEQ ID NOs: 61-68).

FIG. 4 shows multiple sequence alignment of Fc domains from human IgGisotypes using Clustal 2.1. Hinge regions are indicated by dottedunderline. Double underline indicates examples of positions engineeredin IgG1 Fc to promote asymmetric chain pairing and the correspondingpositions with respect to other isotypes IgG2, IgG3 and IgG4.

FIG. 5 shows the purification of ActRIIA-hFc expressed in CHO cells. Theprotein purifies as a single, well-defined peak as visualized by sizingcolumn (top panel) and Coomassie stained SDS-PAGE (bottom panel) (leftlane: molecular weight standards; right lane: ActRIIA-hFc).

FIG. 6 shows the binding of ActRIIA-hFc to activin (top panel) andGDF-11 (bottom panel), as measured by Biacore™ assay.

FIG. 7 shows the full, unprocessed amino acid sequence forActRIIB(25-131)-hFc (SEQ ID NO: 69). The TPA leader (residues 1-22) anddouble-truncated ActRIIB extracellular domain (residues 24-131, usingnumbering based on the native sequence in SEQ ID NO: 1) are eachunderlined. Highlighted is the glutamate revealed by sequencing to bethe N-terminal amino acid of the mature fusion protein, which is atposition 25 relative to SEQ ID NO: 1.

FIGS. 8A and 8B show a nucleotide sequence encoding ActRIIB(25-131)-hFc(the coding strand is shown at top, SEQ ID NO: 70, and the complementshown at bottom 3′-5′, SEQ ID NO: 71). Sequences encoding the TPA leader(nucleotides 1-66) and ActRIIB extracellular domain (nucleotides 73-396)are underlined. The corresponding amino acid sequence forActRIIB(25-131) is also shown.

FIGS. 9A and 9B show an alternative nucleotide sequence encodingActRIIB(25-131)-hFc (the coding strand is shown at top, SEQ ID NO: 72,and the complement shown at bottom 3′-5′, SEQ ID NO: 73). This sequenceconfers a greater level of protein expression in initial transformants,making cell line development a more rapid process. Sequences encodingthe TPA leader (nucleotides 1-66) and ActRIIB extracellular domain(nucleotides 73-396) are underlined, and substitutions in the wild typenucleotide sequence of the ECD (see FIG. 8) are highlighted. Thecorresponding amino acid sequence for ActRIIB(25-131) is also shown.

FIG. 10 shows the full amino acid sequence for the GDF trap ActRIIB(L79D20-134)-hFc (SEQ ID NO: 74), including the TPA leader sequence (doubleunderline), ActRIIB extracellular domain (residues 20-134 in SEQ ID NO:1; single underline), and hFc domain. The aspartate substituted atposition 79 in the native sequence is double underlined and highlighted,as is the glycine revealed by sequencing to be the N-terminal residue inthe mature fusion protein.

FIGS. 11A and 11B shows a nucleotide sequence encoding ActRIIB(L79D20-134)-hFc. SEQ ID NO: 75 corresponds to the sense strand, and SEQ IDNO: 76 corresponds to the antisense strand. The TPA leader (nucleotides1-66) is double underlined, and the ActRIIB extracellular domain(nucleotides 76-420) is single underlined.

FIG. 12 shows the full amino acid sequence for the truncated GDF trapActRIIB(L79D 25-131)-hFc (SEQ ID NO: 77), including the TPA leader(double underline), truncated ActRIIB extracellular domain (residues25-131 in SEQ ID NO:1; single underline), and hFc domain. The aspartatesubstituted at position 79 in the native sequence is double underlinedand highlighted, as is the glutamate revealed by sequencing to be theN-terminal residue in the mature fusion protein.

FIG. 13 shows the amino acid sequence for the truncated GDF trapActRIIB(L79D 25-131)-hFc without a leader (SEQ ID NO: 78). The truncatedActRIIB extracellular domain (residues 25-131 in SEQ ID NO: 1) isunderlined. The aspartate substituted at position 79 in the nativesequence is double underlined and highlighted, as is the glutamaterevealed by sequencing to be the N-terminal residue in the mature fusionprotein.

FIG. 14 shows the amino acid sequence for the truncated GDF trapActRIIB(L79D 25-131) without the leader, hFc domain, and linker (SEQ IDNO: 79). The aspartate substituted at position 79 in the native sequenceis underlined and highlighted, as is the glutamate revealed bysequencing to be the N-terminal residue in the mature fusion protein.

FIGS. 15A and 15B shows a nucleotide sequence encoding ActRIIB(L79D25-131)-hFc. SEQ ID NO: 80 corresponds to the sense strand, and SEQ IDNO: 81 corresponds to the antisense strand. The TPA leader (nucleotides1-66) is double underlined, and the truncated ActRIIB extracellulardomain (nucleotides 76-396) is single underlined. The amino acidsequence for the ActRIIB extracellular domain (residues 25-131 in SEQ IDNO: 1) is also shown.

FIGS. 16A and 16B shows an alternative nucleotide sequence encodingActRIIB(L79D 25-131)-hFc. SEQ ID NO: 82 corresponds to the sense strand,and SEQ ID NO: 83 corresponds to the antisense strand. The TPA leader(nucleotides 1-66) is double underlined, the truncated ActRIIBextracellular domain (nucleotides 76-396) is underlined, andsubstitutions in the wild-type nucleotide sequence of the extracellulardomain are double underlined and highlighted (compare with SEQ ID NO:81, FIG. 15). The amino acid sequence for the ActRIIB extracellulardomain (residues 25-131 in SEQ ID NO: 1) is also shown.

FIG. 17 shows nucleotides 76-396 (SEQ ID NO: 84) of the alternativenucleotide sequence shown in FIG. 16 (SEQ ID NO: 82). The samenucleotide substitutions indicated in FIG. 16 are also underlined andhighlighted here. SEQ ID NO: 84 encodes only the truncated ActRIIBextracellular domain (corresponding to residues 25-131 in SEQ ID NO: 1)with a L79D substitution, e.g., ActRIIB(L79D 25-131).

FIG. 18 shows a multiple sequence alignment of various vertebrate ALK4proteins and human ALK4 (SEQ ID NOs: 126-132).

FIG. 19 shows comparative ligand binding data for an ALK4-Fc:ActRIIB-Fcheterodimeric protein complex compared to ActRIIB-Fc homodimer andALK4-Fc homodimer. For each protein complex, ligands are ranked byk_(off), a kinetic constant that correlates well with ligand signalinginhibition, and listed in descending order of binding affinity (ligandsbound most tightly are listed at the top). At left, yellow, red, green,and blue lines indicate magnitude of the off-rate constant. Solid blacklines indicate ligands whose binding to heterodimer is enhanced orunchanged compared with homodimer, whereas dashed red lines indicatesubstantially reduced binding compared with homodimer. As shown, theALK4-Fc:ActRIIB-Fc heterodimer displays enhanced binding to activin Bcompared with either homodimer, retains strong binding to activin A,GDF8, and GDF11 as observed with ActRIIB-Fc homodimer, and exhibitssubstantially reduced binding to BMP9, BMP10, and GDF3. Like ActRIIB-Fchomodimer, the heterodimer retains intermediate-level binding to BMP6.

FIG. 20 shows comparative ALK4-Fc:ActRIIB-Fcheterodimer/ActRIIB-Fc:ActRIIB-Fc homodimer IC₅₀ data as determined byan A-204 Reporter Gene Assay as described herein. ALK4-Fc:ActRIIB-Fcheterodimer inhibits activin A, activin B, GDF8, and GDF11 signalingpathways similarly to the ActRIIB-Fc:ActRIIB-Fc homodimer. However,ALK4-Fc:ActRIIB-Fc heterodimer inhibition of BMP9 and BMP10 signalingpathways is significantly reduced compared to the ActRIIB-Fc:ActRIIB-Fchomodimer. These data demonstrate that ALK4:ActRIIB heterodimers aremore selective antagonists of activin A, activin B, GDF8, and GDF11compared to corresponding ActRIIB:ActRIIB homodimers.

FIGS. 21A and 21B show two schematic examples of heteromeric proteincomplexes comprising type I receptor and type II receptor polypeptides.FIG. 21A depicts a heterodimeric protein complex comprising one type Ireceptor fusion polypeptide and one type II receptor fusion polypeptide,which can be assembled covalently or noncovalently via a multimerizationdomain contained within each polypeptide chain. Two assembledmultimerization domains constitute an interaction pair, which can beeither guided or unguided. FIG. 21B depicts a heterotetrameric proteincomplex comprising two heterodimeric complexes as depicted in FIG. 21A.Complexes of higher order can be envisioned.

FIG. 22 show a schematic example of a heteromeric protein complexcomprising a type I receptor polypeptide (indicated as “I”) (e.g. apolypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain ofan ALK4 protein from humans or other species such as those describedherein) and a type II receptor polypeptide (indicated as “II”) (e.g. apolypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain ofan ActRIIB protein from humans or other species as such as thosedescribed herein). In the illustrated embodiments, the type I receptorpolypeptide is part of a fusion polypeptide that comprises a firstmember of an interaction pair (“C₁”), and the type II receptorpolypeptide is part of a fusion polypeptide that comprises a secondmember of an interaction pair (“C₂”). In each fusion polypeptide, alinker may be positioned between the type I or type II receptorpolypeptide and the corresponding member of the interaction pair. Thefirst and second members of the interaction pair may be a guided(asymmetric) pair, meaning that the members of the pair associatepreferentially with each other rather than self-associate, or theinteraction pair may be unguided, meaning that the members of the pairmay associate with each other or self-associate without substantialpreference and may have the same or different amino acid sequences.Traditional Fc fusion proteins and antibodies are examples of unguidedinteraction pairs, whereas a variety of engineered Fc domains have beendesigned as guided (asymmetric) interaction pairs [e.g., Spiess et al(2015) Molecular Immunology 67(2A): 95-106].

FIGS. 23A-23D show schematic examples of heteromeric protein complexescomprising an ALK4 polypeptide (e.g. a polypeptide that is at least 70%,75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99% or 100%identical to an extracellular domain of an ALK4 protein from humans orother species such as those described herein) and an ActRIIB polypeptide(e.g. a polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 97%, 98%, 99% or 100% identical to an extracellulardomain of an ActRIIB protein from humans or other species such as thosedescribed herein). In the illustrated embodiments, the ALK4 polypeptideis part of a fusion polypeptide that comprises a first member of aninteraction pair (“C₁”), and the ActRIIB polypeptide is part of a fusionpolypeptide that comprises a second member of an interaction pair(“C₂”). Suitable interaction pairs included, for example, heavy chainand/or light chain immunoglobulin interaction pairs, truncations, andvariants thereof such as those described herein [e.g., Spiess et al(2015) Molecular Immunology 67(2A): 95-106]. In each fusion polypeptide,a linker may be positioned between the ALK4 or ActRIIB polypeptide andthe corresponding member of the interaction pair. The first and secondmembers of the interaction pair may be unguided, meaning that themembers of the pair may associate with each other or self-associatewithout substantial preference, and they may have the same or differentamino acid sequences. See FIG. 23A. Alternatively, the interaction pairmay be a guided (asymmetric) pair, meaning that the members of the pairassociate preferentially with each other rather than self-associate. SeeFIG. 23B. Complexes of higher order can be envisioned. See FIGS. 23C and23D.

DETAILED DESCRIPTION OF THE INVENTION 1. Overview

The TGF-β superfamily is comprised of over 30 secreted factors includingTGF-betas, activins, nodals, bone morphogenetic proteins (BMPs), growthand differentiation factors (GDFs), and anti-Mullerian hormone (AMH)[Weiss et al. (2013) Developmental Biology, 2(1): 47-63]. Members of thesuperfamily, which are found in both vertebrates and invertebrates, areubiquitously expressed in diverse tissues and function during theearliest stages of development throughout the lifetime of an animal.Indeed, TGF-β superfamily proteins are key mediators of stem cellself-renewal, gastrulation, differentiation, organ morphogenesis, andadult tissue homeostasis. Consistent with this ubiquitous activity,aberrant TGF-beta superfamily signaling is associated with a wide rangeof human pathologies including, for example, autoimmune disease,cardiovascular disease, fibrotic disease, and cancer.

Ligands of the TGF-beta superfamily share the same dimeric structure inwhich the central 3½ turn helix of one monomer packs against the concavesurface formed by the beta-strands of the other monomer. The majority ofTGF-beta family members are further stabilized by an intermoleculardisulfide bond. This disulfide bonds traverses through a ring formed bytwo other disulfide bonds generating what has been termed a ‘cysteineknot’ motif [Lin et al. (2006) Reproduction 132: 179-190; and Hinck etal. (2012) FEBS Letters 586: 1860-1870].

TGF-beta superfamily signaling is mediated by heteromeric complexes oftype I and type II serine/threonine kinase receptors, whichphosphorylate and activate downstream SMAD proteins (e.g., SMAD proteins1, 2, 3, 5, and 8) upon ligand stimulation [Massague (2000) Nat. Rev.Mol. Cell Biol. 1:169-178]. These type I and type II receptors aretransmembrane proteins, composed of a ligand-binding extracellulardomain with cysteine-rich region, a transmembrane domain, and acytoplasmic domain with predicted serine/threonine kinase specificity.In general, type I receptors mediate intracellular signaling while thetype II receptors are required for binding TGF-beta superfamily ligands.Type I and II receptors form a stable complex after ligand binding,resulting in phosphorylation of type I receptors by type II receptors.

The TGF-beta family can be divided into two phylogenetic branches basedon the type I receptors they bind and the Smad proteins they activate.One is the more recently evolved branch, which includes, e.g., theTGF-betas, activins, GDF8, GDF9, GDF11, BMP3 and nodal, which signalthrough type I receptors that activate Smads 2 and 3 [Hinck (2012) FEBSLetters 586:1860-1870]. The other branch comprises the more distantlyrelated proteins of the superfamily and includes, e.g., BMP2, BMP4,BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF1, GDF5, GDF6, and GDF7,which signal through Smads 1, 5, and 8.

Activins are members of the TGF-beta superfamily and were initiallydiscovered as regulators of secretion of follicle-stimulating hormone,but subsequently various reproductive and non-reproductive roles havebeen characterized. There are three principal activin forms (A, B, andAB) that are homo/heterodimers of two closely related β subunits(β_(A)β_(A), β_(B)β_(B), and β_(A)β_(B), respectively). The human genomealso encodes an activin C and an activin E, which are primarilyexpressed in the liver, and heterodimeric forms containing β_(C) orβ_(E) are also known. In the TGF-beta superfamily, activins are uniqueand multifunctional factors that can stimulate hormone production inovarian and placental cells, support neuronal cell survival, influencecell-cycle progress positively or negatively depending on cell type, andinduce mesodermal differentiation at least in amphibian embryos [DePaoloet al. (1991) Proc Soc Ep Biol Med. 198:500-512; Dyson et al. (1997)Curr Biol. 7:81-84; and Woodruff (1998) Biochem Pharmacol. 55:953-963].In several tissues, activin signaling is antagonized by its relatedheterodimer, inhibin. For example, in the regulation offollicle-stimulating hormone (FSH) secretion from the pituitary, activinpromotes FSH synthesis and secretion, while inhibin reduces FSHsynthesis and secretion. Other proteins that may regulate activinbioactivity and/or bind to activin include follistatin (FS),follistatin-related protein (FSRP, also known as FLRG or FSTL3), andα₂-macroglobulin.

As described herein, agents that bind to “activin A” are agents thatspecifically bind to the β_(A) subunit, whether in the context of anisolated β_(A) subunit or as a dimeric complex (e.g., a β_(A)β_(A)homodimer or a β_(A)β_(B) heterodimer). In the case of a heterodimercomplex (e.g., a β_(A)β_(B) heterodimer), agents that bind to “activinA” are specific for epitopes present within the PA subunit, but do notbind to epitopes present within the non-β_(A) subunit of the complex(e.g., the β_(B) subunit of the complex). Similarly, agents disclosedherein that antagonize (inhibit) “activin A” are agents that inhibit oneor more activities as mediated by a β_(A) subunit, whether in thecontext of an isolated β_(A) subunit or as a dimeric complex (e.g., aβ_(A)β_(A) homodimer or a β_(A)N heterodimer). In the case of β_(A)β_(B)heterodimers, agents that inhibit “activin A” are agents thatspecifically inhibit one or more activities of the β_(A) subunit, but donot inhibit the activity of the non-β_(A) subunit of the complex (e.g.,the β_(B) subunit of the complex). This principle applies also to agentsthat bind to and/or inhibit “activin B”, “activin C”, and “activin E”.Agents disclosed herein that antagonize “activin AB” are agents thatinhibit one or more activities as mediated by the β_(A) subunit and oneor more activities as mediated by the β_(B) subunit.

The BMPs and GDFs together form a family of cysteine-knot cytokinessharing the characteristic fold of the TGF-beta superfamily [Rider etal. (2010) Biochem J., 429(1):1-12]. This family includes, for example,BMP2, BMP4, BMP6, BMP7, BMP2a, BMP3, BMP3b (also known as GDF10), BMP4,BMP5, BMP6, BMP7, BMP8, BMP8a, BMP8b, BMP9 (also known as GDF2), BMP10,BMP11 (also known as GDF11), BMP12 (also known as GDF7), BMP13 (alsoknown as GDF6), BMP14 (also known as GDF5), BMP15, GDF1, GDF3 (alsoknown as VGR2), GDF8 (also known as myostatin), GDF9, GDF15, anddecapentaplegic. Besides the ability to induce bone formation, whichgave the BMPs their name, the BMP/GDFs display morphogenetic activitiesin the development of a wide range of tissues. BMP/GDF homo- andhetero-dimers interact with combinations of type I and type II receptordimers to produce multiple possible signaling complexes, leading to theactivation of one of two competing sets of SMAD transcription factors.BMP/GDFs have highly specific and localized functions. These areregulated in a number of ways, including the developmental restrictionof BMP/GDF expression and through the secretion of several specific BMPantagonist proteins that bind with high affinity to the cytokines.Curiously, a number of these antagonists resemble TGF-beta superfamilyligands.

Growth and differentiation factor-8 (GDF8) is also known as myostatin.GDF8 is a negative regulator of skeletal muscle mass and is highlyexpressed in developing and adult skeletal muscle. The GDF8 nullmutation in transgenic mice is characterized by a marked hypertrophy andhyperplasia of skeletal muscle [McPherron et al. Nature (1997)387:83-90]. Similar increases in skeletal muscle mass are evident innaturally occurring mutations of GDF8 in cattle and, strikingly, inhumans [Ashmore et al. (1974) Growth, 38:501-507; Swatland and Kieffer,J. Anim. Sci. (1994) 38:752-757; McPherron and Lee, Proc. Natl. Acad.Sci. USA (1997) 94:12457-12461; Kambadur et al. Genome Res. (1997)7:910-915; and Schuelke et al. (2004) N Engl J Med, 350:2682-8]. Studieshave also shown that muscle wasting associated with HIV-infection inhumans is accompanied by increases in GDF8 protein expression[Gonzalez-Cadavid et al., PNAS (1998) 95:14938-43]. In addition, GDF8can modulate the production of muscle-specific enzymes (e.g., creatinekinase) and modulate myoblast cell proliferation [International PatentApplication Publication No. WO 00/43781]. The GDF8 propeptide cannoncovalently bind to the mature GDF8 domain dimer, inactivating itsbiological activity [Miyazono et al. (1988) J. Biol. Chem., 263:6407-6415; Wakefield et al. (1988) J. Biol. Chem., 263; 7646-7654; andBrown et al. (1990) Growth Factors, 3: 35-43]. Other proteins which bindto GDF8 or structurally related proteins and inhibit their biologicalactivity include follistatin, and potentially, follistatin-relatedproteins [Gamer et al. (1999) Dev. Biol., 208: 222-232].

GDF11, also known as BMP11, is a secreted protein that is expressed inthe tail bud, limb bud, maxillary and mandibular arches, and dorsal rootganglia during mouse development [McPherron et al. (1999) Nat. Genet.,22: 260-264; and Nakashima et al. (1999) Mech. Dev., 80: 185-189]. GDF11plays a unique role in patterning both mesodermal and neural tissues[Gamer et al. (1999) Dev Biol., 208:222-32]. GDF11 was shown to be anegative regulator of chondrogenesis and myogenesis in developing chicklimb [Gamer et al. (2001) Dev Biol., 229:407-20]. The expression ofGDF11 in muscle also suggests its role in regulating muscle growth in asimilar way to GDF8. In addition, the expression of GDF11 in brainsuggests that GDF11 may also possess activities that relate to thefunction of the nervous system. Interestingly, GDF11 was found toinhibit neurogenesis in the olfactory epithelium [Wu et al. (2003)Neuron., 37:197-207]. Hence, GDF11 may have in vitro and in vivoapplications in the treatment of diseases such as muscle diseases andneurodegenerative diseases (e.g., amyotrophic lateral sclerosis).

As demonstrated herein, a soluble ActRIIA polypeptide and ALK4:ActRIIBheterodimer, which both bind to various ActRIIA and ActRIIB-interactingligands, is effective in decreasing blood pressure and cardiachypertrophy in a PAH model. While not wishing to be bound to anyparticular mechanism, it is expected that the effects of these agents iscaused primarily by an ActRIIA/B signaling antagonist effect. Regardlessof the mechanism, it is apparent from the data presented herein thatActRIIA/B signaling antagonists (GDF/BMP antagonists) do decrease bloodpressure, decrease cardiac hypertrophy, and have other positivityeffects in treating pulmonary hypertension. It should be noted thatblood pressure and hypertrophy are dynamic, with changes depending on abalance of factors that increase blood pressure and hypertrophy andfactors that decrease blood pressure and hypertrophy. Blood pressure andcardiac hypertrophy can be decreased by increasing factors that reduceblood pressure and cardiac hypertrophy, decreasing factors that promoteelevated blood pressure and cardiac hypertrophy, or both. The termsdecreasing blood pressure or decreasing cardiac hypertrophy refer to theobservable physical changes in blood pressure and cardiac tissue and areintended to be neutral as to the mechanism by which the changes occur.

The rat models for PAH that were used in the studies described hereinare considered to be predicative of efficacy in humans, and therefore,this disclosure provides methods for using ActRIIA polypeptides,ALK4:ActRIIB heteromultimers, and other GDF/BMP antagonists to treatpulmonary hypertension (e.g., PAH), particularly treating, preventing,or reducing the severity or duration of one or more complications ofpulmonary hypertension, in humans. As disclosed herein, the term GDF/BMPantagonists refers a variety of agents that may be used to antagonizeActRIIA/B signaling including, for example, antagonists that inhibit oneor more ActRIIA/B ligands [e.g., activin (activin A, activin B, activinAB, activin C, activin AC, activin BC, activin E, activin AE, and/oractivin BE), GDF8, GDF11, GDF3, BMP6, BMP15, BMP10]; antagonists thatinhibit one or more type I and/or type II receptors (e.g., ActRIIA,ActRIIB, ALK4, ALK7, and ALK5); and antagonists that inhibit one or moredownstream signaling components (e.g., Smad proteins such as Smads 2 and3). GDF/BMP antagonists to be used in accordance with the methods anduses of the disclosure include a variety of forms, for example, ligandtraps (e.g., soluble ActRIIA polypeptides, ActRIIB polypeptides,ALK4:ActRIIB heterodimers, follistatin polypeptides, and FLRGpolypeptides), antibody antagonists (e.g., antibodies that inhibit oneor more of activin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA,ActRIIB, ALK4, ALK7, and ALK5), small molecule antagonists [e.g., smallmolecules that inhibit one or more of activin, GDF8, GDF11, GDF3, BMP6,BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK7, ALK5, and one or more Smadproteins (e.g., Smads 2 and 3)], and nucleotide antagonists [e.g.,nucleotide sequences that inhibit one or more of activin, GDF8, GDF11,GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK7, ALK5, and one ormore Smad proteins (e.g., Smads 2 and 3)].

The terms used in this specification generally have their ordinarymeanings in the art, within the context of this disclosure and in thespecific context where each term is used. Certain terms are discussedbelow or elsewhere in the specification to provide additional guidanceto the practitioner in describing the compositions and methods of thedisclosure and how to make and use them. The scope or meaning of any useof a term will be apparent from the specific context in which it isused.

“Homologous,” in all its grammatical forms and spelling variations,refers to the relationship between two proteins that possess a “commonevolutionary origin,” including proteins from superfamilies in the samespecies of organism, as well as homologous proteins from differentspecies of organism. Such proteins (and their encoding nucleic acids)have sequence homology, as reflected by their sequence similarity,whether in terms of percent identity or by the presence of specificresidues or motifs and conserved positions. However, in common usage andin the instant application, the term “homologous,” when modified with anadverb such as “highly,” may refer to sequence similarity and may or maynot relate to a common evolutionary origin.

The term “sequence similarity,” in all its grammatical forms, refers tothe degree of identity or correspondence between nucleic acid or aminoacid sequences that may or may not share a common evolutionary origin.

“Percent (%) sequence identity” with respect to a reference polypeptide(or nucleotide) sequence is defined as the percentage of amino acidresidues (or nucleic acids) in a candidate sequence that are identicalto the amino acid residues (or nucleic acids) in the referencepolypeptide (nucleotide) sequence, after aligning the sequences andintroducing gaps, if necessary, to achieve the maximum percent sequenceidentity, and not considering any conservative substitutions as part ofthe sequence identity. Alignment for purposes of determining percentamino acid sequence identity can be achieved in various ways that arewithin the skill in the art, for instance, using publicly availablecomputer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR)software. Those skilled in the art can determine appropriate parametersfor aligning sequences, including any algorithms needed to achievemaximal alignment over the full length of the sequences being compared.For purposes herein, however, % amino acid (nucleic acid) sequenceidentity values are generated using the sequence comparison computerprogram ALIGN-2. The ALIGN-2 sequence comparison computer program wasauthored by Genentech, Inc., and the source code has been filed withuser documentation in the U.S. Copyright Office, Washington D.C., 20559,where it is registered under U.S. Copyright Registration No. TXU510087.The ALIGN-2 program is publicly available from Genentech, Inc., SouthSan Francisco, Calif., or may be compiled from the source code. TheALIGN-2 program should be compiled for use on a UNIX operating system,including digital UNIX V4.0D. All sequence comparison parameters are setby the ALIGN-2 program and do not vary.

“Agonize”, in all its grammatical forms, refers to the process ofactivating a protein and/or gene (e.g., by activating or amplifying thatprotein's gene expression or by inducing an inactive protein to enter anactive state) or increasing a protein's and/or gene's activity.

“Antagonize”, in all its grammatical forms, refers to the process ofinhibiting a protein and/or gene (e.g., by inhibiting or decreasing thatprotein's gene expression or by inducing an active protein to enter aninactive state) or decreasing a protein's and/or gene's activity.

The terms “about” and “approximately” as used in connection with anumerical value throughout the specification and the claims denotes aninterval of accuracy, familiar and acceptable to a person skilled in theart. In general, such interval of accuracy is ±10%. Alternatively, andparticularly in biological systems, the terms “about” and“approximately” may mean values that are within an order of magnitude,preferably ≦5-fold and more preferably ≦2-fold of a given value.

Numeric ranges disclosed herein are inclusive of the numbers definingthe ranges. The terms “a” and “an” include plural referents unless thecontext in which the term is used clearly dictates otherwise. The terms“a” (or “an”), as well as the terms “one or more,” and “at least one”can be used interchangeably herein. Furthermore, “and/or” where usedherein is to be taken as specific disclosure of each of the two or morespecified features or components with or without the other. Thus, theterm “and/or” as used in a phrase such as “A and/or B” herein isintended to include “A and B,” “A or B,” “A” (alone), and “B” (alone).Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C”is intended to encompass each of the following aspects: A, B, and C; A,B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B(alone); and C (alone).

Throughout this specification, the word “comprise” or variations such as“comprises” or “comprising” will be understood to imply the inclusion ofa stated integer or groups of integers but not the exclusion of anyother integer or group of integers.

2. ActRII Polypeptides, ALK4 Polypeptides, ALK4:ActRIIB Heteromultimers,and Variants Thereof

In certain aspects, the disclosure relates ActRII polypeptides and usesthereof (e.g., of treating, preventing, or reducing the progression rateand/or severity of pulmonary hypertension or one or more complicationsof pulmonary hypertension) and/or an interstitial lung disease (e.g.,idiopathic pulmonary fibrosis). As used herein, the term “ActRII” refersto the family of type II activin receptors. This family includes activinreceptor type IIA (ActRIIA) and activin receptor type IIB (ActRIIB)

As used herein, the term “ActRIIB” refers to a family of activinreceptor type IIB (ActRIIB) proteins from any species and variantsderived from such ActRIIB proteins by mutagenesis or other modification.Reference to ActRIIB herein is understood to be a reference to any oneof the currently identified forms. Members of the ActRIIB family aregenerally transmembrane proteins, composed of a ligand-bindingextracellular domain comprising a cysteine-rich region, a transmembranedomain, and a cytoplasmic domain with predicted serine/threonine kinaseactivity.

The term “ActRIIB polypeptide” includes polypeptides comprising anynaturally occurring polypeptide of an ActRIIB family member as well asany variants thereof (including mutants, fragments, fusions, andpeptidomimetic forms) that retain a useful activity. Examples of suchvariant ActRIIB polypeptides are provided throughout the presentdisclosure as well as in International Patent Application PublicationNos. WO 2006/012627, WO 2008/097541, WO 2010/151426, and WO 2011/020045,which are incorporated herein by reference in their entirety. Numberingof amino acids for all ActRIIB-related polypeptides described herein isbased on the numbering of the human ActRIIB precursor protein sequenceprovided below (SEQ ID NO: 1), unless specifically designated otherwise.

The human ActRIIB precursor protein sequence is as follows:

(SEQ ID NO: 1)   1 MTAPWVALAL LWGSLCAGS G RGEAETRECI YYNANWELER T NQSGLERCE  51 GEQDKRLHCY ASWR N SSGTI ELVKKGCWLD DFNCYDRQEC VATEENPQVY101 FCCCEGNFCN ERFTHLPEAG GPEVTYEPPP TAPTLLTVLA YSLLPIGGLS 151LIVLLAFWMY RHRKPPYGHV DIHEDPGPPP PSPLVGLKPL QLLEIKARGR 201FGCVWKAQLM NDFVAVKIFP LQDKQSWQSE REIFSTPGMK HENLLQFIAA 251EKRGSNLEVE LWLITAFHDK GSLTDYLKGN IITWNELCHV AETMSRGLSY 301LHEDVPWCRG EGHKPSIAHR DFKSKNVLLK SDLTAVLADF GLAVRFEPGK 351PPGDTHGQVG TRRYMAPEVL EGAINFQRDA FLRIDMYAMG LVLWELVSRC 401KAADGPVDEY MLPFEEEIGQ HPSLEELQEV VVHKKMRPTI KDHWLKHPGL 451AQLCVTIEEC WDHDAEARLS AGCVEERVSL IRRSVNGTTS DCLVSLVTSV 501 TNVDLPPKES SI

The signal peptide is indicated with a single underline; theextracellular domain is indicated in bold font; and the potential,endogenous N-linked glycosylation sites are indicated with a doubleunderline.

The processed (mature) extracellular ActRIIB polypeptide sequence is asfollows:

(SEQ ID NO: 2) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEA GGPEVTYEPPPTAPT.

In some embodiments, the protein may be produced with an “SGR . . . ”sequence at the N-terminus. The C-terminal “tail” of the extracellulardomain is indicated by a single underline. The sequence with the “tail”deleted (a 415 sequence) is as follows:

(SEQ ID NO: 3) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPE A.

A form of ActRIIB with an alanine at position 64 of SEQ ID NO: 1 (A64)is also reported in the literature. See, e.g., Hilden et al. (1994)Blood, 83(8): 2163-2170. Applicants have ascertained that an ActRIIB-Fcfusion protein comprising an extracellular domain of ActRIIB with theA64 substitution has a relatively low affinity for activin and GDF11. Bycontrast, the same ActRIIB-Fc fusion protein with an arginine atposition 64 (R64) has an affinity for activin and GDF11 in the lownanomolar to high picomolar range. Therefore, sequences with an R64 areused as the “wild-type” reference sequence for human ActRIIB in thisdisclosure.

The form of ActRIIB with an alanine at position 64 is as follows:

(SEQ ID NO: 4)   1 MTAPWVALAL LWGSLCAGSG RGEAETRECI YYNANWELER TNQSGLERCE  51GEQDKRLHCY ASWANSSGTI ELVKKGCWLD DFNCYDRQEC VATEENPQVY 101FCCCEGNFCN ERFTHLPEAG GPEVTYEPPP TAPTLLTVLA YSLLPIGGLS 151LIVLLAFWMY RHRKPPYGHV DIHEDPGPPP PSPLVGLKPL QLLEIKARGR 201FGCVWKAQLM NDFVAVKIFP LQDKQSWQSE REIFSTPGMK HENLLQFIAA 251EKRGSNLEVE LWLITAFHDK GSLTDYLKGN IITWNELCHV AETMSRGLSY 301LHEDVPWCRG EGHKPSIAHR DFKSKNVLLK SDLTAVLADF GLAVRFEPGK 351PPGDTHGQVG TRRYMAPEVL EGAINFQRDA FLRIDMYAMG LVLWELVSRC 401KAADGPVDEY MLPFEEEIGQ HPSLEELQEV VVHKKMRPTI KDHWLKHPGL 451AQLCVTIEEC WDHDAEARLS AGCVEERVSL IRRSVNGTTS DCLVSLVTSV 501 TNVDLPPKES SI

The signal peptide is indicated by single underline and theextracellular domain is indicated by bold font.

The processed (mature) extracellular ActRIIB polypeptide sequence of thealternative A64 form is as follows:

(SEQ ID NO: 5) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWANSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLP EAGGPEVTYEPPPTAPT

In some embodiments, the protein may be produced with an “SGR . . . ”sequence at the N-terminus. The C-terminal “tail” of the extracellulardomain is indicated by single underline. The sequence with the “tail”deleted (a 415 sequence) is as follows:

(SEQ ID NO: 6) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWANSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLP EA

A nucleic acid sequence encoding the human ActRIIB precursor protein isshown below (SEQ ID NO: 7), representing nucleotides 25-1560 of GenbankReference Sequence NM_001106.3, which encode amino acids 1-513 of theActRIIB precursor. The sequence as shown provides an arginine atposition 64 and may be modified to provide an alanine instead.

The signal sequence is underlined.

(SEQ ID NO: 7)    1ATGACGGCGC CCTGGGTGGC CCTCGCCCTC CTCTGGGGAT CGCTGTGCGC   51CGGCTCTGGG CGTGGGGAGG CTGAGACACG GGAGTGCATC TACTACAACG  101CCAACTGGGA GCTGGAGCGC ACCAACCAGA GCGGCCTGGA GCGCTGCGAA  151GGCGAGCAGG ACAAGCGGCT GCACTGCTAC GCCTCCTGGC GCAACAGCTC  201TGGCACCATC GAGCTCGTGA AGAAGGGCTG CTGGCTAGAT GACTTCAACT  251GCTACGATAG GCAGGAGTGT GTGGCCACTG AGGAGAACCC CCAGGTGTAC  301TTCTGCTGCT GTGAAGGCAA CTTCTGCAAC GAACGCTTCA CTCATTTGCC  351AGAGGCTGGG GGCCCGGAAG TCACGTACGA GCCACCCCCG ACAGCCCCCA  401CCCTGCTCAC GGTGCTGGCC TACTCACTGC TGCCCATCGG GGGCCTTTCC  451CTCATCGTCC TGCTGGCCTT TTGGATGTAC CGGCATCGCA AGCCCCCCTA  501CGGTCATGTG GACATCCATG AGGACCCTGG GCCTCCACCA CCATCCCCTC  551TGGTGGGCCT GAAGCCACTG CAGCTGCTGG AGATCAAGGC TCGGGGGCGC  601TTTGGCTGTG TCTGGAAGGC CCAGCTCATG AATGACTTTG TAGCTGTCAA  651GATCTTCCCA CTCCAGGACA AGCAGTCGTG GCAGAGTGAA CGGGAGATCT  701TCAGCACACC TGGCATGAAG CACGAGAACC TGCTACAGTT CATTGCTGCC  751GAGAAGCGAG GCTCCAACCT CGAAGTAGAG CTGTGGCTCA TCACGGCCTT  801CCATGACAAG GGCTCCCTCA CGGATTACCT CAAGGGGAAC ATCATCACAT  851GGAACGAACT GTGTCATGTA GCAGAGACGA TGTCACGAGG CCTCTCATAC  901CTGCATGAGG ATGTGCCCTG GTGCCGTGGC GAGGGCCACA AGCCGTCTAT  951TGCCCACAGG GACTTTAAAA GTAAGAATGT ATTGCTGAAG AGCGACCTCA 1001CAGCCGTGCT GGCTGACTTT GGCTTGGCTG TTCGATTTGA GCCAGGGAAA 1051CCTCCAGGGG ACACCCACGG ACAGGTAGGC ACGAGACGGT ACATGGCTCC 1101TGAGGTGCTC GAGGGAGCCA TCAACTTCCA GAGAGATGCC TTCCTGCGCA 1151TTGACATGTA TGCCATGGGG TTGGTGCTGT GGGAGCTTGT GTCTCGCTGC 1201AAGGCTGCAG ACGGACCCGT GGATGAGTAC ATGCTGCCCT TTGAGGAAGA 1251GATTGGCCAG CACCCTTCGT TGGAGGAGCT GCAGGAGGTG GTGGTGCACA 1301AGAAGATGAG GCCCACCATT AAAGATCACT GGTTGAAACA CCCGGGCCTG 1351GCCCAGCTTT GTGTGACCAT CGAGGAGTGC TGGGACCATG ATGCAGAGGC 1401TCGCTTGTCC GCGGGCTGTG TGGAGGAGCG GGTGTCCCTG ATTCGGAGGT 1451CGGTCAACGG CACTACCTCG GACTGTCTCG TTTCCCTGGT GACCTCTGTC 1501ACCAATGTGG ACCTGCCCCC TAAAGAGTCA AGCATC

A nucleic acid sequence encoding processed extracellular human ActRIIBpolypeptide is as follows (SEQ ID NO: 8). The sequence as shown providesan arginine at position 64, and may be modified to provide an alanineinstead.

(SEQ ID NO: 8) 1 GGGCGTGGGG AGGCTGAGAC ACGGGAGTGC ATCTACTACA ACGCCAACTG51 GGAGCTGGAG CGCACCAACC AGAGCGGCCT GGAGCGCTGC GAAGGCGAGC 101AGGACAAGCG GCTGCACTGC TACGCCTCCT GGCGCAACAG CTCTGGCACC 151ATCGAGCTCG TGAAGAAGGG CTGCTGGCTA GATGACTTCA ACTGCTACGA 201TAGGCAGGAG TGTGTGGCCA CTGAGGAGAA CCCCCAGGTG TACTTCTGCT 251GCTGTGAAGG CAACTTCTGC AACGAACGCT TCACTCATTT GCCAGAGGCT 301GGGGGCCCGG AAGTCACGTA CGAGCCACCC CCGACAGCCC CCACC

An alignment of the amino acid sequences of human ActRIIB extracellulardomain and human ActRIIA extracellular domain are illustrated in FIG. 1.This alignment indicates amino acid residues within both receptors thatare believed to directly contact ActRII ligands. For example, thecomposite ActRII structures indicated that the ActRIIB-ligand bindingpocket is defined, in part, by residues Y31, N33, N35, L38 through T41,E47, E50, Q53 through K55, L57, H58, Y60, S62, K74, W78 through N83,Y85, R87, A92, and E94 through F101. At these positions, it is expectedthat conservative mutations will be tolerated.

In addition, ActRIIB is well-conserved among vertebrates, with largestretches of the extracellular domain completely conserved. For example,FIG. 2 depicts a multi-sequence alignment of a human ActRIIBextracellular domain compared to various ActRIIB orthologs. Many of theligands that bind to ActRIIB are also highly conserved. Accordingly,from these alignments, it is possible to predict key amino acidpositions within the ligand-binding domain that are important for normalActRIIB-ligand binding activities as well as to predict amino acidpositions that are likely to be tolerant to substitution withoutsignificantly altering normal ActRIIB-ligand binding activities.Therefore, an active, human ActRIIB variant polypeptide useful inaccordance with the presently disclosed methods may include one or moreamino acids at corresponding positions from the sequence of anothervertebrate ActRIIB, or may include a residue that is similar to that inthe human or other vertebrate sequences. Without meaning to be limiting,the following examples illustrate this approach to defining an activeActRIIB variant. L46 in the human extracellular domain (SEQ ID NO: 2) isa valine in Xenopus ActRIIB (SEQ ID NO: 58), and so this position may bealtered, and optionally may be altered to another hydrophobic residue,such as V, I or F, or a non-polar residue such as A. E52 in the humanextracellular domain is a K in Xenopus, indicating that this site may betolerant of a wide variety of changes, including polar residues, such asE, D, K, R, H, S, T, P, G, Y and probably A. T93 in the humanextracellular domain is a K in Xenopus, indicating that a widestructural variation is tolerated at this position, with polar residuesfavored, such as S, K, R, E, D, H, G, P, G and Y. F108 in the humanextracellular domain is a Y in Xenopus, and therefore Y or otherhydrophobic group, such as I, V or L should be tolerated. E111 in thehuman extracellular domain is K in Xenopus, indicating that chargedresidues will be tolerated at this position, including D, R, K and H, aswell as Q and N. R112 in the human extracellular domain is K in Xenopus,indicating that basic residues are tolerated at this position, includingR and H. A at position 119 in the human extracellular domain isrelatively poorly conserved, and appears as P in rodents and V inXenopus, thus essentially any amino acid should be tolerated at thisposition.

Moreover, ActRII proteins have been characterized in the art in terms ofstructural and functional characteristics, particularly with respect toligand binding [Attisano et al. (1992) Cell 68(1):97-108; Greenwald etal. (1999) Nature Structural Biology 6(1): 18-22; Allendorph et al.(2006) PNAS 103(20: 7643-7648; Thompson et al. (2003) The EMBO Journal22(7): 1555-1566; as well as U.S. Pat. Nos. 7,709,605, 7,612,041, and7,842,663]. In addition to the teachings herein, these referencesprovide amply guidance for how to generate ActRIIB variants that retainone or more normal activities (e.g., ligand-binding activity).

For example, a defining structural motif known as a three-finger toxinfold is important for ligand binding by type I and type II receptors andis formed by conserved cysteine residues located at varying positionswithin the extracellular domain of each monomeric receptor [Greenwald etal. (1999) Nat Struct Biol 6:18-22; and Hinck (2012) FEBS Lett586:1860-1870]. Accordingly, the core ligand-binding domains of humanActRIIB, as demarcated by the outermost of these conserved cysteines,corresponds to positions 29-109 of SEQ ID NO: 1 (ActRIIB precursor). Thestructurally less-ordered amino acids flanking these cysteine-demarcatedcore sequences can be truncated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28residues at the N-terminus and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 residues a the C-terminuswithout necessarily altering ligand binding. Exemplary ActRIIBextracellular domains for N-terminal and/or C-terminal truncationinclude SEQ ID NOs: 2, 3, 5, and 6.

Attisano et al. showed that a deletion of the proline knot at theC-terminus of the extracellular domain of ActRIIB reduced the affinityof the receptor for activin. An ActRIIB-Fc fusion protein containingamino acids 20-119 of present SEQ ID NO: 1, “ActRIIB(20-119)-Fc”, hasreduced binding to GDF11 and activin relative to an ActRIIB(20-134)-Fc,which includes the proline knot region and the complete juxtamembranedomain (see, e.g., U.S. Pat. No. 7,842,663). However, anActRIIB(20-129)-Fc protein retains similar, but somewhat reducedactivity, relative to the wild-type, even though the proline knot regionis disrupted.

Thus, ActRIIB extracellular domains that stop at amino acid 134, 133,132, 131, 130 and 129 (with respect to SEQ ID NO: 1) are all expected tobe active, but constructs stopping at 134 or 133 may be most active.Similarly, mutations at any of residues 129-134 (with respect to SEQ IDNO: 1) are not expected to alter ligand-binding affinity by largemargins. In support of this, it is known in the art that mutations ofP129 and P130 (with respect to SEQ ID NO: 1) do not substantiallydecrease ligand binding. Therefore, an ActRIIB polypeptide of thepresent disclosure may end as early as amino acid 109 (the finalcysteine), however, forms ending at or between 109 and 119 (e.g., 109,110, 111, 112, 113, 114, 115, 116, 117, 118, or 119) are expected tohave reduced ligand binding. Amino acid 119 (with respect to present SEQID NO:1) is poorly conserved and so is readily altered or truncated.ActRIIB polypeptides ending at 128 (with respect to SEQ ID NO: 1) orlater should retain ligand-binding activity. ActRIIB polypeptides endingat or between 119 and 127 (e.g., 119, 120, 121, 122, 123, 124, 125, 126,or 127), with respect to SEQ ID NO: 1, will have an intermediate bindingability. Any of these forms may be desirable to use, depending on theclinical or experimental setting.

At the N-terminus of ActRIIB, it is expected that a protein beginning atamino acid 29 or before (with respect to SEQ ID NO: 1) will retainligand-binding activity. Amino acid 29 represents the initial cysteine.An alanine-to-asparagine mutation at position 24 (with respect to SEQ IDNO: 1) introduces an N-linked glycosylation sequence withoutsubstantially affecting ligand binding [U.S. Pat. No. 7,842,663]. Thisconfirms that mutations in the region between the signal cleavagepeptide and the cysteine cross-linked region, corresponding to aminoacids 20-29, are well tolerated. In particular, ActRIIB polypeptidesbeginning at position 20, 21, 22, 23, and 24 (with respect to SEQ IDNO: 1) should retain general ligand-biding activity, and ActRIIBpolypeptides beginning at positions 25, 26, 27, 28, and 29 (with respectto SEQ ID NO: 1) are also expected to retain ligand-biding activity. Ithas been demonstrated, e.g., U.S. Pat. No. 7,842,663, that,surprisingly, an ActRIIB construct beginning at 22, 23, 24, or 25 willhave the most activity.

Taken together, a general formula for an active portion (e.g.,ligand-binding portion) of ActRIIB comprises amino acids 29-109 of SEQID NO: 1. Therefore ActRIIB polypeptides may, for example, comprise,consists essentially of, or consists of an amino acid sequence that isat least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIBbeginning at a residue corresponding to any one of amino acids 20-29(e.g., beginning at any one of amino acids 20, 21, 22, 23, 24, 25, 26,27, 28, or 29) of SEQ ID NO: 1 and ending at a position corresponding toany one amino acids 109-134 (e.g., ending at any one of amino acids 109,110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134) of SEQ IDNO: 1. Other examples include polypeptides that begin at a position from20-29 (e.g., any one of positions 20, 21, 22, 23, 24, 25, 26, 27, 28, or29) or 21-29 (e.g., any one of positions 21, 22, 23, 24, 25, 26, 27, 28,or 29) of SEQ ID NO: 1 and end at a position from 119-134 (e.g., any oneof positions 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,131, 132, 133, or 134), 119-133 (e.g., any one of positions 119, 120,121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, or 133),129-134 (e.g., any one of positions 129, 130, 131, 132, 133, or 134), or129-133 (e.g., any one of positions 129, 130, 131, 132, or 133) of SEQID NO: 1. Other examples include constructs that begin at a positionfrom 20-24 (e.g., any one of positions 20, 21, 22, 23, or 24), 21-24(e.g., any one of positions 21, 22, 23, or 24), or 22-25 (e.g., any oneof positions 22, 22, 23, or 25) of SEQ ID NO: 1 and end at a positionfrom 109-134 (e.g., any one of positions 109, 110, 111, 112, 113, 114,115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,129, 130, 131, 132, 133, or 134), 119-134 (e.g., any one of positions119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, or 134) or 129-134 (e.g., any one of positions 129, 130, 131, 132,133, or 134) of SEQ ID NO: 1. Variants within these ranges are alsocontemplated, particularly those comprising, consisting essentially of,or consisting of an amino acid sequence that has at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identity to the corresponding portion of SEQ ID NO: 1.

The variations described herein may be combined in various ways. In someembodiments, ActRIIB variants comprise no more than 1, 2, 5, 6, 7, 8, 9,10 or 15 conservative amino acid changes in the ligand-binding pocket,optionally zero, one or more non-conservative alterations at positions40, 53, 55, 74, 79 and/or 82 in the ligand-binding pocket. Sites outsidethe binding pocket, at which variability may be particularly welltolerated, include the amino and carboxy termini of the extracellulardomain (as noted above), and positions 42-46 and 65-73 (with respect toSEQ ID NO: 1). An asparagine-to-alanine alteration at position 65 (N65A)does not appear to decrease ligand binding in the R64 background [U.S.Pat. No. 7,842,663]. This change probably eliminates glycosylation atN65 in the A64 background, thus demonstrating that a significant changein this region is likely to be tolerated. While an R64A change is poorlytolerated, R64K is well-tolerated, and thus another basic residue, suchas H may be tolerated at position 64 [U.S. Pat. No. 7,842,663].Additionally, the results of the mutagenesis program described in theart indicate that there are amino acid positions in ActRIIB that areoften beneficial to conserve. With respect to SEQ ID NO: 1, theseinclude position 80 (acidic or hydrophobic amino acid), position 78(hydrophobic, and particularly tryptophan), position 37 (acidic, andparticularly aspartic or glutamic acid), position 56 (basic amino acid),position 60 (hydrophobic amino acid, particularly phenylalanine ortyrosine). Thus, the disclosure provides a framework of amino acids thatmay be conserved in ActRIIB polypeptides. Other positions that may bedesirable to conserve are as follows: position 52 (acidic amino acid),position 55 (basic amino acid), position 81 (acidic), 98 (polar orcharged, particularly E, D, R or K), all with respect to SEQ ID NO: 1.

It has been previously demonstrated that the addition of a furtherN-linked glycosylation site (N-X-S/T) into the ActRIIB extracellulardomain is well-tolerated (see, e.g., U.S. Pat. No. 7,842,663).Therefore, N-X-S/T sequences may be generally introduced at positionsoutside the ligand binding pocket defined in FIG. 1 in ActRIIBpolypeptide of the present disclosure. Particularly suitable sites forthe introduction of non-endogenous N-X-S/T sequences include amino acids20-29, 20-24, 22-25, 109-134, 120-134 or 129-134 (with respect to SEQ IDNO: 1). N-X-S/T sequences may also be introduced into the linker betweenthe ActRIIB sequence and an Fc domain or other fusion component as wellas optionally into the fusion component itself. Such a site may beintroduced with minimal effort by introducing an N in the correctposition with respect to a pre-existing S or T, or by introducing an Sor T at a position corresponding to a pre-existing N. Thus, desirablealterations that would create an N-linked glycosylation site are: A24N,R64N, S67N (possibly combined with an N65A alteration), E105N, R112N,G120N, E123N, P129N, A132N, R112S and R112T (with respect to SEQ ID NO:1). Any S that is predicted to be glycosylated may be altered to a Twithout creating an immunogenic site, because of the protection affordedby the glycosylation. Likewise, any T that is predicted to beglycosylated may be altered to an S. Thus the alterations S67T and S44T(with respect to SEQ ID NO: 1) are contemplated. Likewise, in an A24Nvariant, an S26T alteration may be used. Accordingly, an ActRIIBpolypeptide of the present disclosure may be a variant having one ormore additional, non-endogenous N-linked glycosylation consensussequences as described above.

In certain embodiments, the disclosure relates to GDF/BMP antagonists(inhibitors) that comprise a ActRIIB polypeptide, which includesfragments, functional variants, and modified forms thereof as well asuses thereof (e.g., treating or preventing PH or one or morePH-associated complication). Preferably, ActRIIB polypeptides aresoluble (e.g., comprise an extracellular domain of ActRIIB) In someembodiments, ActRIIB polypeptides antagonize activity (e.g., Smadsignaling) of one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin(activin A, activin B, activin AB, activin C, activin E) BMP6, GDF3,BMP15, and BMP10]. Therefore, in some embodiments, ActRIIB polypeptidesbind to one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin (activinA, activin B, activin AB, activin C, activin E) BMP6, GDF3, BMP15, andBMP10]. In some embodiments, ActRIIB polypeptides of the disclosurecomprise, consist essentially of, or consist of an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion ofActRIIB beginning at a residue corresponding to amino acids 20-29 (e.g.,beginning at any one of amino acids 20, 21, 22, 23, 24, 25, 26, 27, 28,or 29) of SEQ ID NO: 1 and ending at a position corresponding to aminoacids 109-134 (e.g., ending at any one of amino acids 109, 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, or 134) of SEQ ID NO: 1. In someembodiments, ActRIIB polypeptides comprise, consist, or consistessentially of an amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical amino acids 29-109 of SEQ ID NO: 1. In someembodiments, ActRIIB polypeptides of the disclosure comprise, consist,or consist essentially of an amino acid sequence that is at least 70%,75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or 100% identical amino acids 29-109 of SEQ ID NO: 1,wherein the position corresponding to L79 of SEQ ID NO: 1 is an acidicamino acid (naturally occurring acidic amino acids D and E or anartificial acidic amino acid). In certain embodiments, ActRIIBpolypeptides of the disclosure comprise, consist, or consist essentiallyof an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical amino acids 25-131 of SEQ ID NO: 1. In certain embodiments,ActRIIB polypeptides of the disclosure comprise, consist, or consistessentially of an amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical amino acids 25-131 of SEQ ID NO: 1, wherein theposition corresponding to L79 of SEQ ID NO: 1 is an acidic amino acid.In some embodiments, ActRIIB polypeptide of disclosure comprise,consist, or consist essentially of an amino acid sequence that is atleast 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of anyone of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 40, 42, 45, 46, 47, 48, 69, 74, 77,78, 79, 108, 110, 114, 115, 118, and 120. In some embodiments, ActRIIBpolypeptide of disclosure comprise, consist, or consist essentially ofan amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99%, or 100% identicalto the amino acid sequence of any one of SEQ ID NOs: 1, 2, 3, 4, 5, 6,40, 42, 45, 46, 47, 48, 69, 74, 77, 78, 79, 108, 110, 114, 115, 118, and120, wherein the position corresponding to L79 of SEQ ID NO: 1 is anacidic amino acid. In some embodiments, ActRIIB polypeptides of thedisclosure comprise, consist, or consist essentially of, at least oneActRIIB polypeptide wherein the position corresponding to L79 of SEQ IDNO: 1 is not an acidic amino acid (i.e., is not naturally occurring acidamino acids D or E or an artificial acidic amino acid residue).

In certain embodiments, the present disclosure relates to ActRIIApolypeptides. As used herein, the term “ActRIIA” refers to a family ofactivin receptor type IIA (ActRIIA) proteins from any species andvariants derived from such ActRIIA proteins by mutagenesis or othermodification. Reference to ActRIIA herein is understood to be areference to any one of the currently identified forms. Members of theActRIIA family are generally transmembrane proteins, composed of aligand-binding extracellular domain comprising a cysteine-rich region, atransmembrane domain, and a cytoplasmic domain with predictedserine/threonine kinase activity.

The term “ActRIIA polypeptide” includes polypeptides comprising anynaturally occurring polypeptide of an ActRIIA family member as well asany variants thereof (including mutants, fragments, fusions, andpeptidomimetic forms) that retain a useful activity. Examples of suchvariant ActRIIA polypeptides are provided throughout the presentdisclosure as well as in International Patent Application PublicationNos. WO 2006/012627 and WO 2007/062188, which are incorporated herein byreference in their entirety. Numbering of amino acids for allActRIIA-related polypeptides described herein is based on the numberingof the human ActRIIA precursor protein sequence provided below (SEQ IDNO: 9), unless specifically designated otherwise.

The canonical human ActRIIA precursor protein sequence is as follows:

(SEQ ID NO: 9) 1 MGAAAKLAFA VFLISCSSGA ILGRSETQEC LFFNANWEKD RT NQTGVEPC 51 YGDKDKRRHC FATWK N ISGS IEIVKQGCWL DDINCYDRTD CVEKKDSPEV 101YFCCCEGNMC NEKFSYFPEM EVTQPTSNPV TPKPPYYNIL LYSLVPLMLI 151AGIVICAFWV YRHHKMAYPP VLVPTQDPGP PPPSPLLGLK PLQLLEVKAR 201GRFGCVWKAQ LLNEYVAVKI FPIQDKQSWQ NEYEVYSLPG MKHENILQFI 251GAEKRGTSVD VDLWLITAFH EKGSLSDFLK ANVVSWNELC HIAETMARGL 301AYLHEDIPGL KDGHKPAISH RDIKSKNVLL KNNLTACIAD FGLALKFEAG 351KSAGDTHGQV GTRRYMAPEV LEGAINFQRD AFLRIDMYAM GLVLWELASR 401CTAADGPVDE YMLPFEEEIG QHPSLEDMQE VVVHKKKRPV LRDYWQKHAG 451MAMLCETIEE CWDHDAEARL SAGCVGERIT QMQRLTNIIT TEDIVTVVTM 501VTNVDFPPKE SSL

The signal peptide is indicated by a single underline; the extracellulardomain is indicated in bold font; and the potential, endogenous N-linkedglycosylation sites are indicated by a double underline.

The processed (mature) extracellular human ActRIIA polypeptide sequenceis as follows:

(SEQ ID NO: 10) ILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEM EVTQPTSNPVTPKPP

The C-terminal “tail” of the extracellular domain is indicated by singleunderline. The sequence with the “tail” deleted (a 415 sequence) is asfollows:

(SEQ ID NO: 11) ILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEM

The nucleic acid sequence encoding human ActRIIA precursor protein isshown below (SEQ ID NO: 12), as follows nucleotides 159-1700 of GenbankReference Sequence NM_001616.4. The signal sequence is underlined.

(SEQ ID NO: 12) 1 ATGGGAGCTG CTGCAAAGTT GGCGTTTGCC GTCTTTCTTA TCTCCTGTTC51 TTCAGGTGCT ATACTTGGTA GATCAGAAAC TCAGGAGTGT CTTTTCTTTA 101ATGCTAATTG GGAAAAAGAC AGAACCAATC AAACTGGTGT TGAACCGTGT 151TATGGTGACA AAGATAAACG GCGGCATTGT TTTGCTACCT GGAAGAATAT 201TTCTGGTTCC ATTGAAATAG TGAAACAAGG TTGTTGGCTG GATGATATCA 251ACTGCTATGA CAGGACTGAT TGTGTAGAAA AAAAAGACAG CCCTGAAGTA 301TATTTTTGTT GCTGTGAGGG CAATATGTGT AATGAAAAGT TTTCTTATTT 351TCCGGAGATG GAAGTCACAC AGCCCACTTC AAATCCAGTT ACACCTAAGC 401CACCCTATTA CAACATCCTG CTCTATTCCT TGGTGCCACT TATGTTAATT 451GCGGGGATTG TCATTTGTGC ATTTTGGGTG TACAGGCATC ACAAGATGGC 501CTACCCTCCT GTACTTGTTC CAACTCAAGA CCCAGGACCA CCCCCACCTT 551CTCCATTACT AGGTTTGAAA CCACTGCAGT TATTAGAAGT GAAAGCAAGG 601GGAAGATTTG GTTGTGTCTG GAAAGCCCAG TTGCTTAACG AATATGTGGC 651TGTCAAAATA TTTCCAATAC AGGACAAACA GTCATGGCAA AATGAATACG 701AAGTCTACAG TTTGCCTGGA ATGAAGCATG AGAACATATT ACAGTTCATT 751GGTGCAGAAA AACGAGGCAC CAGTGTTGAT GTGGATCTTT GGCTGATCAC 801AGCATTTCAT GAAAAGGGTT CACTATCAGA CTTTCTTAAG GCTAATGTGG 851TCTCTTGGAA TGAACTGTGT CATATTGCAG AAACCATGGC TAGAGGATTG 901GCATATTTAC ATGAGGATAT ACCTGGCCTA AAAGATGGCC ACAAACCTGC 951CATATCTCAC AGGGACATCA AAAGTAAAAA TGTGCTGTTG AAAAACAACC 1001TGACAGCTTG CATTGCTGAC TTTGGGTTGG CCTTAAAATT TGAGGCTGGC 1051AAGTCTGCAG GCGATACCCA TGGACAGGTT GGTACCCGGA GGTACATGGC 1101TCCAGAGGTA TTAGAGGGTG CTATAAACTT CCAAAGGGAT GCATTTTTGA 1151GGATAGATAT GTATGCCATG GGATTAGTCC TATGGGAACT GGCTTCTCGC 1201TGTACTGCTG CAGATGGACC TGTAGATGAA TACATGTTGC CATTTGAGGA 1251GGAAATTGGC CAGCATCCAT CTCTTGAAGA CATGCAGGAA GTTGTTGTGC 1301ATAAAAAAAA GAGGCCTGTT TTAAGAGATT ATTGGCAGAA ACATGCTGGA 1351ATGGCAATGC TCTGTGAAAC CATTGAAGAA TGTTGGGATC ACGACGCAGA 1401AGCCAGGTTA TCAGCTGGAT GTGTAGGTGA AAGAATTACC CAGATGCAGA 1451GACTAACAAA TATTATTACC ACAGAGGACA TTGTAACAGT GGTCACAATG 1501GTGACAAATG TTGACTTTCC TCCCAAAGAA TCTAGTCTA

The nucleic acid sequence encoding processed soluble (extracellular)human ActRIIA polypeptide is as follows:

(SEQ ID NO: 13) 1 ATACTTGGTA GATCAGAAAC TCAGGAGTGT CTTTTCTTTA ATGCTAATTG51 GGAAAAAGAC AGAACCAATC AAACTGGTGT TGAACCGTGT TATGGTGACA 101AAGATAAACG GCGGCATTGT TTTGCTACCT GGAAGAATAT TTCTGGTTCC 151ATTGAAATAG TGAAACAAGG TTGTTGGCTG GATGATATCA ACTGCTATGA 201CAGGACTGAT TGTGTAGAAA AAAAAGACAG CCCTGAAGTA TATTTTTGTT 251GCTGTGAGGG CAATATGTGT AATGAAAAGT TTTCTTATTT TCCGGAGATG 301GAAGTCACAC AGCCCACTTC AAATCCAGTT ACACCTAAGC CACCC

ActRIIA is well-conserved among vertebrates, with large stretches of theextracellular domain completely conserved. For example, FIG. 3 depicts amulti-sequence alignment of a human ActRIIA extracellular domaincompared to various ActRIIA orthologs. Many of the ligands that bind toActRIIA are also highly conserved. Accordingly, from these alignments,it is possible to predict key amino acid positions within theligand-binding domain that are important for normal ActRIIA-ligandbinding activities as well as to predict amino acid positions that arelikely to be tolerant to substitution without significantly alteringnormal ActRIIA-ligand binding activities. Therefore, an active, humanActRIIA variant polypeptide useful in accordance with the presentlydisclosed methods may include one or more amino acids at correspondingpositions from the sequence of another vertebrate ActRIIA, or mayinclude a residue that is similar to that in the human or othervertebrate sequences.

Without meaning to be limiting, the following examples illustrate thisapproach to defining an active ActRIIA variant. As illustrated in FIG.3, F13 in the human extracellular domain is Y in Ovis aries (SEQ ID NO:62), Gallus gallus (SEQ ID NO: 65), Bos Taurus (SEQ ID NO: 66), Tytoalba (SEQ ID NO: 67), and Myotis davidii (SEQ ID NO: 68) ActRIIA,indicating that aromatic residues are tolerated at this position,including F, W, and Y. Q24 in the human extracellular domain is R in BosTaurus ActRIIA, indicating that charged residues will be tolerated atthis position, including D, R, K, H, and E. S95 in the humanextracellular domain is F in Gallus gallus and Tyto alba ActRIIA,indicating that this site may be tolerant of a wide variety of changes,including polar residues, such as E, D, K, R, H, S, T, P, G, Y, andprobably hydrophobic residue such as L, I, or F. E52 in the humanextracellular domain is D in Ovis aries ActRIIA, indicating that acidicresidues are tolerated at this position, including D and E. P29 in thehuman extracellular domain is relatively poorly conserved, appearing asS in Ovis aries ActRIIA and L in Myotis davidii ActRIIA, thusessentially any amino acid should be tolerated at this position.

Moreover, as discussed above, ActRII proteins have been characterized inthe art in terms of structural/functional characteristics, particularlywith respect to ligand binding [Attisano et al. (1992) Cell68(1):97-108; Greenwald et al. (1999) Nature Structural Biology 6(1):18-22; Allendorph et al. (2006) PNAS 103(20: 7643-7648; Thompson et al.(2003) The EMBO Journal 22(7): 1555-1566; as well as U.S. Pat. Nos.7,709,605, 7,612,041, and 7,842,663]. In addition to the teachingsherein, these references provide amply guidance for how to generateActRII variants that retain one or more desired activities (e.g.,ligand-binding activity).

For example, a defining structural motif known as a three-finger toxinfold is important for ligand binding by type I and type II receptors andis formed by conserved cysteine residues located at varying positionswithin the extracellular domain of each monomeric receptor [Greenwald etal. (1999) Nat Struct Biol 6:18-22; and Hinck (2012) FEBS Lett586:1860-1870]. Accordingly, the core ligand-binding domains of humanActRIIA, as demarcated by the outermost of these conserved cysteines,corresponds to positions 30-110 of SEQ ID NO: 9 (ActRIIA precursor).Therefore, the structurally less-ordered amino acids flanking thesecysteine-demarcated core sequences can be truncated by about 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, or 29 residues at the N-terminus and by about 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, or 25 residues at the C-terminus without necessarily alteringligand binding. Exemplary ActRIIA extracellular domains truncationsinclude SEQ ID NOs: 10 and 11.

Accordingly, a general formula for an active portion (e.g., ligandbinding) of ActRIIA is a polypeptide that comprises, consistsessentially of, or consists of amino acids 30-110 of SEQ ID NO: 9.Therefore ActRIIA polypeptides may, for example, comprise, consistsessentially of, or consists of an amino acid sequence that is at least70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIA beginningat a residue corresponding to any one of amino acids 21-30 (e.g.,beginning at any one of amino acids 21, 22, 23, 24, 25, 26, 27, 28, 29,or 30) of SEQ ID NO: 9 and ending at a position corresponding to any oneamino acids 110-135 (e.g., ending at any one of amino acids 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, or 135) of SEQ ID NO: 9.Other examples include constructs that begin at a position selected from21-30 (e.g., beginning at any one of amino acids 21, 22, 23, 24, 25, 26,27, 28, 29, or 30), 22-30 (e.g., beginning at any one of amino acids 22,23, 24, 25, 26, 27, 28, 29, or 30), 23-30 (e.g., beginning at any one ofamino acids 23, 24, 25, 26, 27, 28, 29, or 30), 24-30 (e.g., beginningat any one of amino acids 24, 25, 26, 27, 28, 29, or 30) of SEQ ID NO:9, and end at a position selected from 111-135 (e.g., ending at any oneof amino acids 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134 or 135),112-135 (e.g., ending at any one of amino acids 112, 113, 114, 115, 116,117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,131, 132, 133, 134 or 135), 113-135 (e.g., ending at any one of aminoacids 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134 or 135), 120-135 (e.g.,ending at any one of amino acids 120, 121, 122, 123, 124, 125, 126, 127,128, 129, 130, 131, 132, 133, 134 or 135), 130-135 (e.g., ending at anyone of amino acids 130, 131, 132, 133, 134 or 135), 111-134 (e.g.,ending at any one of amino acids 110, 111, 112, 113, 114, 115, 116, 117,118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,132, 133, or 134), 111-133 (e.g., ending at any one of amino acids 110,111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,125, 126, 127, 128, 129, 130, 131, 132, or 133), 111-132 (e.g., endingat any one of amino acids 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, or132), or 111-131 (e.g., ending at any one of amino acids 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,127, 128, 129, 130, or 131) of SEQ ID NO: 9. Variants within theseranges are also contemplated, particularly those comprising, consistingessentially of, or consisting of an amino acid sequence that has atleast 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identity to the corresponding portionof SEQ ID NO: 9. Thus, in some embodiments, an ActRIIA polypeptide maycomprise, consists essentially of, or consist of a polypeptide that isat least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids 30-110 ofSEQ ID NO: 9. Optionally, ActRIIA polypeptides comprise a polypeptidethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids30-110 of SEQ ID NO: 9, and comprising no more than 1, 2, 5, 10 or 15conservative amino acid changes in the ligand-binding pocket.

In certain embodiments, the disclosure relates to GDF/BMP antagonists(inhibitors) that comprise an ActRIIA polypeptide, which includesfragments, functional variants, and modified forms thereof as well asuses thereof (e.g., increasing an immune response in a patient in needthereof and treating cancer). Preferably, ActRIIA polypeptides aresoluble (e.g., an extracellular domain of ActRIIA). In some embodiments,ActRIIA polypeptides inhibit (e.g., Smad signaling) of one or moreGDF/BMP ligands [e.g., GDF11, GDF8, activin (activin A, activin B,activin AB, activin C, activin E) BMP6, GDF3, BMP15, and/or BMP10]. Insome embodiments, ActRIIA polypeptides bind to one or more GDF/BMPligands [e.g., GDF11, GDF8, activin (activin A, activin B, activin AB,activin C, activin E) BMP6, GDF3, BMP15, and/or BMP10]. In someembodiments, ActRIIA polypeptide of the disclosure comprise, consistessentially of, or consist of an amino acid sequence that is at least70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIA beginningat a residue corresponding to amino acids 21-30 (e.g., beginning at anyone of amino acids 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) of SEQ IDNO: 9 and ending at a position corresponding to any one amino acids110-135 (e.g., ending at any one of amino acids 110, 111, 112, 113, 114,115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,129, 130, 131, 132, 133, 134 or 135) of SEQ ID NO: 9. In someembodiments, ActRIIA polypeptides comprise, consist, or consistessentially of an amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical amino acids 30-110 of SEQ ID NO: 9. In certainembodiments, ActRIIA polypeptides comprise, consist, or consistessentially of an amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical amino acids 21-135 of SEQ ID NO: 9. In someembodiments, ActRIIA polypeptides comprise, consist, or consistessentially of an amino acid sequence that is at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99%, or100% identical to the amino acid sequence of any one of SEQ ID NOs: 9,10, 11, 32, 36, and 39.

In certain aspects, the present disclosure relates to GDF trappolypeptides (also referred to as “GDF traps”). In some embodiments, GDFtraps of the present disclosure are variant ActRII polypeptides (e.g.,ActRIIA and ActRIIB polypeptides) that comprise one or more mutations(e.g., amino acid additions, deletions, substitutions, and combinationsthereof) in the extracellular domain (also referred to as theligand-binding domain) of an ActRII polypeptide (e.g., a “wild-type” orunmodified ActRII polypeptide) such that the variant ActRII polypeptidehas one or more altered ligand-binding activities than the correspondingwild-type ActRII polypeptide. In preferred embodiments, GDF trappolypeptides of the present disclosure retain at least one similaractivity as a corresponding wild-type ActRII polypeptide. For example,preferable GDF traps bind to and inhibit (e.g. antagonize) the functionof GDF11 and/or GDF8. In some embodiments, GDF traps of the presentdisclosure further bind to and inhibit one or more of ligand of theGDF/BMP. Accordingly, the present disclosure provides GDF trappolypeptides that have an altered binding specificity for one or moreActRII ligands.

To illustrate, one or more mutations may be selected that increase theselectivity of the altered ligand-binding domain for GDF11 and/or GDF8over one or more ActRII-binding ligands such as activins (activin A,activin B, activin AB, activin C, and/or activin E), particularlyactivin A. Optionally, the altered ligand-binding domain has a ratio ofK_(d) for activin binding to K_(d) for GDF11 and/or GDF8 binding that isat least 2-, 5-, 10-, 20-, 50-, 100- or even 1000-fold greater relativeto the ratio for the wild-type ligand-binding domain. Optionally, thealtered ligand-binding domain has a ratio of IC₅₀ for inhibiting activinto IC₅₀ for inhibiting GDF11 and/or GDF8 that is at least 2-, 5-, 10-,20-, 50-, 100- or even 1000-fold greater relative to the wild-typeligand-binding domain. Optionally, the altered ligand-binding domaininhibits GDF11 and/or GDF8 with an IC₅₀ at least 2-, 5-, 10-, 20-, 50-,100- or even 1000-times less than the IC₅₀ for inhibiting activin.

Amino acid residues of the ActRIIB proteins (e.g., E39, K55, Y60, K74,W78, L79, D80, and F101 with respect to SEQ ID NO: 1) are in the ActRIIBligand-binding pocket and help mediated binding to its ligandsincluding, for example, activin A, GDF11, and GDF8. Thus the presentdisclosure provides GDF trap polypeptides comprising an altered-ligandbinding domain (e.g., a GDF8/GDF11-binding domain) of an ActRIIBreceptor which comprises one or more mutations at those amino acidresidues.

As a specific example, the positively-charged amino acid residue Asp(D80) of the ligand-binding domain of ActRIIB can be mutated to adifferent amino acid residue to produce a GDF trap polypeptide thatpreferentially binds to GDF8, but not activin. Preferably, the D80residue with respect to SEQ ID NO: 1 is changed to an amino acid residueselected from the group consisting of: an uncharged amino acid residue,a negative amino acid residue, and a hydrophobic amino acid residue. Asa further specific example, the hydrophobic residue L79 of SEQ ID NO: 1can be altered to confer altered activin-GDF11/GDF8 binding properties.For example, an L79P substitution reduces GDF11 binding to a greaterextent than activin binding. In contrast, replacement of L79 with anacidic amino acid [an aspartic acid or glutamic acid; an L79D or an L79Esubstitution] greatly reduces activin A binding affinity while retainingGDF11 binding affinity. In exemplary embodiments, the methods describedherein utilize a GDF trap polypeptide which is a variant ActRIIBpolypeptide comprising an acidic amino acid (e.g., D or E) at theposition corresponding to position 79 of SEQ ID NO: 1, optionally incombination with one or more additional amino acid substitutions,additions, or deletions.

In certain aspects, the disclosure relates ALK4 polypeptides and usesthereof. As used herein, the term “ALK4” refers to a family of activinreceptor-like kinase-4 proteins from any species and variants derivedfrom such ALK4 proteins by mutagenesis or other modification. Referenceto ALK4 herein is understood to be a reference to any one of thecurrently identified forms. Members of the ALK4 family are generallytransmembrane proteins, composed of a ligand-binding extracellulardomain with a cysteine-rich region, a transmembrane domain, and acytoplasmic domain with predicted serine/threonine kinase activity.

The term “ALK4 polypeptide” includes polypeptides comprising anynaturally occurring polypeptide of an ALK4 family member as well as anyvariants thereof (including mutants, fragments, fusions, andpeptidomimetic forms) that retain a useful activity. Numbering of aminoacids for all ALK4-related polypeptides described herein is based on thenumbering of the human ALK4 precursor protein sequence below (SEQ ID NO:100), unless specifically designated otherwise.

A human ALK4 precursor protein sequence (NCBI Ref Seq NP_004293) is asfollows:

(SEQ ID NO: 100 1 MAESAGASSF FPLVVLLLAG SGGSGPRGVQ ALLCACTSCL QANYTCETDG ACMVSIFNLD 61GMEHHVRTCI PKVELVPAGK PFYCLSSEDL RNTHCCYTDY CNRIDLRVPS GHLKEPEHPS 121MWGPVELVGI IAGPVFLLFL IIIIVFLVIN YHQRVYHNRQ RLDMEDPSCE MCLSKDKTLQ 181DLVYDLSTSG SGSGLPLFVQ RTVARTIVLQ EIIGKGRFGE VWRGRWRGGD VAVKIFSSRE 241ERSWFREAEI YQTVMLRHEN ILGFIAADNK DNGTWTQLWL VSDYHEHGSL FDYLNRYTVT 301IEGMIKLALS AASGLAHLHM EIVGTQGKPG IAHRDLKSKN ILVKKNGMCA IADLGLAVRH 361DAVTDTIDIA PNQRVGTKRY MAPEVLDETI NMKHFDSFKC ADIYALGLVY WEIARRCNSG 421GVHEEYQLPY YDLVPSDPSI EEMRKVVCDQ KLRPNIPNWW QSYEALRVMG KMMRECWYAN 481GAARLTALRI KKTLSQLSVQ EDVKI

The signal peptide is indicated by a single underline and theextracellular domain is indicated in bold font.

A processed extracellular human ALK4 polypeptide sequence is as follows:

(SEQ ID NO: 101) SGPRGVQALLCACTSCLQANYTCETDGACMVSIFNLDGMEHHVRTCIPKVELVPAGKPFYCLSSEDLRNTHCCYTDYCNRIDLRVPSGHLKEPEHPSMWG PVE

A nucleic acid sequence encoding the ALK4 precursor protein is shownbelow (SEQ ID NO: 102), corresponding to nucleotides 78-1592 of GenbankReference Sequence NM_004302.4. The signal sequence is underlined andthe extracellular domain is indicated in bold font.

(SEQ ID NO: 102) ATGGCGGAGTCGGCCGGAGCCTCCTCCTTCTTCCCCCTTGTTGTCCTCCTGCTCGCCGGCAGCGGCGGG TCCGGGCCCCGGGGGGTCCAGGCTCTGCTGTGTGCGTGCACCAGCTGCCTCCAGGCCAACTACACGTGTGAGACAGATGGGGCCTGCATGGTTTCCATTTTCAATCTGGATGGGATGGAGCACCATGTGCGCACCTGCATCCCCAAAGTGGAGCTGGTCCCTGCCGGGAAGCCCTTCTACTGCCTGAGCTCGGAGGACCTGCGCAACACCCACTGCTGCTACACTGACTACTGCAACAGGATCGACTTGAGGGTGCCCAGTGGTCACCTCAAGGAGCCTGAGCACCCGTCCATGTGGGGCCCGGTGGAGCTGGTAGGCATCATCGCCGGCCCGGTGTTCCTCCTGTTCCTCATCATCATCATTGTTTTCCTTGTCATTAACTATCATCAGCGTGTCTATCACAACCGCCAGAGACTGGACATGGAAGATCCCTCATGTGAGATGTGTCTCTCCAAAGACAAGACGCTCCAGGATCTTGTCTACGATCTCTCCACCTCAGGGTCTGGCTCAGGGTTACCCCTCTTTGTCCAGCGCACAGTGGCCCGAACCATCGTTTTACAAGAGATTATTGGCAAGGGTCGGTTTGGGGAAGTATGGCGGGGCCGCTGGAGGGGTGGTGATGTGGCTGTGAAAATATTCTCTTCTCGTGAAGAACGGTCTTGGTTCAGGGAAGCAGAGATATACCAGACGGTCATGCTGCGCCATGAAAACATCCTTGGATTTATTGCTGCTGACAATAAAGATAATGGCACCTGGACACAGCTGTGGCTTGTTTCTGACTATCATGAGCACGGGTCCCTGTTTGATTATCTGAACCGGTACACAGTGACAATTGAGGGGATGATTAAGCTGGCCTTGTCTGCTGCTAGTGGGCTGGCACACCTGCACATGGAGATCGTGGGCACCCAAGGGAAGCCTGGAATTGCTCATCGAGACTTAAAGTCAAAGAACATTCTGGTGAAGAAAAATGGCATGTGTGCCATAGCAGACCTGGGCCTGGCTGTCCGTCATGATGCAGTCACTGACACCATTGACATTGCCCCGAATCAGAGGGTGGGGACCAAACGATACATGGCCCCTGAAGTACTTGATGAAACCATTAATATGAAACACTTTGACTCCTTTAAATGTGCTGATATTTATGCCCTCGGGCTTGTATATTGGGAGATTGCTCGAAGATGCAATTCTGGAGGAGTCCATGAAGAATATCAGCTGCCATATTACGACTTAGTGCCCTCTGACCCTTCCATTGAGGAAATGCGAAAGGTTGTATGTGATCAGAAGCTGCGTCCCAACATCCCCAACTGGTGGCAGAGTTATGAGGCACTGCGGGTGATGGGGAAGATGATGCGAGAGTGTTGGTATGCCAACGGCGCAGCCCGCCTGACGGCCCTGCGCATCAAGAAGACCCTCTCCCAGCTCAGCGTGCAGGAAGACGTGAAGATC

A nucleic acid sequence encoding the extracellular ALK4 polypeptide isas follows:

(SEQ ID NO: 103) TCCGGGCCCCGGGGGGTCCAGGCTCTGCTGTGTGCGTGCACCAGCTGCCTCCAGGCCAACTACACGTGTGAGACAGATGGGGCCTGCATGGTTTCCATTTTCAATCTGGATGGGATGGAGCACCATGTGCGCACCTGCATCCCCAAAGTGGAGCTGGTCCCTGCCGGGAAGCCCTTCTACTGCCTGAGCTCGGAGGACCTGCGCAACACCCACTGCTGCTACACTGACTACTGCAACAGGATCGACTTGAGGGTGCCCAGTGGTCACCTCAAGGAGCCTGAGCACCCGTCCATGTGGGGC CCGGTGGAG

An alternative isoform of human ALK4 precursor protein sequence, isoformB (NCBI Ref Seq NP_064732.3), is as follows:

(SEQ ID NO: 104) 1MVSIFNLDGM EHHVRTCIPK VELVPAGKPF YCLSSEDLRN THCCYTDYCN RIDLRVPSGH 61LKEPEHPSMW GPVELVGIIA GPVFLLFLII IIVFLVINYH QRVYHNRQRL DMEDPSCEMC 121LSKDKTLQDL VYDLSTSGSG SGLPLFVQRT VARTIVLQEI IGKGRFGEVW RGRWRGGDVA 181VKIFSSREER SWFREAEIYQ TVMLRHENIL GFIAADNKDN GTWTQLWLVS DYHEHGSLFD 241YLNRYTVTIE GMIKLALSAA SGLAHLHMEI VGTQGKPGIA HRDLKSKNIL VKKNGMCAIA 301DLGLAVRHDA VTDTIDIAPN QRVGTKRYMA PEVLDETINM KHFDSFKCAD IYALGLVYWE 361IARRCNSGGV HEEYQLPYYD LVPSDPSIEE MRKVVCDQKL RPNIPNWWQS YEALRVMGKM 421MRECWYANGA ARLTALRIKK TLSQLSVQED VKI

The extracellular domain is indicated in bold font.

A processed extracellular ALK4 polypeptide sequence is as follows:

(SEQ ID NO: 105) 1MVSIFNLDGM EHHVRTCIPK VELVPAGKPF YCLSSEDLRN THCCYTDYCN RIDLRVPSGH 61LKEPEHPSMW GPVE

A nucleic acid sequence encoding the ALK4 precursor protein (isoform B)is shown below (SEQ ID NO: 106), corresponding to nucleotides 186-1547of Genbank Reference Sequence NM_020327.3. The nucleotides encoding theextracellular domain are indicated in bold font.

(SEQ ID NO: 106) 1ATGGTTTCCA TTTTCAATCT GGATGGGATG GAGCACCATG TGCGCACCTG 51CATCCCCAAA GTGGAGCTGG TCCCTGCCGG GAAGCCCTTC TACTGCCTGA 101GCTCGGAGGA CCTGCGCAAC ACCCACTGCT GCTACACTGA CTACTGCAAC 151AGGATCGACT TGAGGGTGCC CAGTGGTCAC CTCAAGGAGC CTGAGCACCC 201GTCCATGTGG GGCCCGGTGG AGCTGGTAGG CATCATCGCC GGCCCGGTGT 251TCCTCCTGTT CCTCATCATC ATCATTGTTT TCCTTGTCAT TAACTATCAT 301CAGCGTGTCT ATCACAACCG CCAGAGACTG GACATGGAAG ATCCCTCATG 351TGAGATGTGT CTCTCCAAAG ACAAGACGCT CCAGGATCTT GTCTACGATC 401TCTCCACCTC AGGGTCTGGC TCAGGGTTAC CCCTCTTTGT CCAGCGCACA 451GTGGCCCGAA CCATCGTTTT ACAAGAGATT ATTGGCAAGG GTCGGTTTGG 501GGAAGTATGG CGGGGCCGCT GGAGGGGTGG TGATGTGGCT GTGAAAATAT 551TCTCTTCTCG TGAAGAACGG TCTTGGTTCA GGGAAGCAGA GATATACCAG 601ACGGTCATGC TGCGCCATGA AAACATCCTT GGATTTATTG CTGCTGACAA 651TAAAGATAAT GGCACCTGGA CACAGCTGTG GCTTGTTTCT GACTATCATG 701AGCACGGGTC CCTGTTTGAT TATCTGAACC GGTACACAGT GACAATTGAG 751GGGATGATTA AGCTGGCCTT GTCTGCTGCT AGTGGGCTGG CACACCTGCA 801CATGGAGATC GTGGGCACCC AAGGGAAGCC TGGAATTGCT CATCGAGACT 851TAAAGTCAAA GAACATTCTG GTGAAGAAAA ATGGCATGTG TGCCATAGCA 901GACCTGGGCC TGGCTGTCCG TCATGATGCA GTCACTGACA CCATTGACAT 951TGCCCCGAAT CAGAGGGTGG GGACCAAACG ATACATGGCC CCTGAAGTAC 1001TTGATGAAAC CATTAATATG AAACACTTTG ACTCCTTTAA ATGTGCTGAT 1051ATTTATGCCC TCGGGCTTGT ATATTGGGAG ATTGCTCGAA GATGCAATTC 1101TGGAGGAGTC CATGAAGAAT ATCAGCTGCC ATATTACGAC TTAGTGCCCT 1151CTGACCCTTC CATTGAGGAA ATGCGAAAGG TTGTATGTGA TCAGAAGCTG 1201CGTCCCAACA TCCCCAACTG GTGGCAGAGT TATGAGGCAC TGCGGGTGAT 1251GGGGAAGATG ATGCGAGAGT GTTGGTATGC CAACGGCGCA GCCCGCCTGA 1301CGGCCCTGCG CATCAAGAAG ACCCTCTCCC AGCTCAGCGT GCAGGAAGAC 1351GTGAAGATCT AA

A nucleic acid sequence encoding the extracellular ALK4 polypeptide(isoform B) is as follows:

(SEQ ID NO: 107) 1ATGGTTTCCA TTTTCAATCT GGATGGGATG GAGCACCATG TGCGCACCTG 51CATCCCCAAA GTGGAGCTGG TCCCTGCCGG GAAGCCCTTC TACTGCCTGA 101GCTCGGAGGA CCTGCGCAAC ACCCACTGCT GCTACACTGA CTACTGCAAC 151AGGATCGACT TGAGGGTGCC CAGTGGTCAC CTCAAGGAGC CTGAGCACCC 201GTCCATGTGG GGCCCGGTGG AGCTGGTAGG

ALK4 is well-conserved among vertebrates, with large stretches of theextracellular domain completely conserved. For example, FIG. 18 depictsa multi-sequence alignment of a human ALK4 extracellular domain comparedto various ALK4 orthologs. Many of the ligands that bind to ALK4 arealso highly conserved. Accordingly, from these alignments, it ispossible to predict key amino acid positions within the ligand-bindingdomain that are important for normal ALK4-ligand binding activities aswell as to predict amino acid positions that are likely to be tolerantto substitution without significantly altering normal ALK4-ligandbinding activities. Therefore, an active, human ALK4 variant polypeptideuseful in accordance with the presently disclosed methods may includeone or more amino acids at corresponding positions from the sequence ofanother vertebrate ALK4, or may include a residue that is similar tothat in the human or other vertebrate sequences.

Without meaning to be limiting, the following examples illustrate thisapproach to defining an active ALK4 variant. As illustrated in FIG. 18,V6 in the human ALK4 extracellular domain (SEQ ID NO: 126) is isoleucinein Mus muculus ALK4 (SEQ ID NO: 130), and so the position may bealtered, and optionally may be altered to another hydrophobic residuesuch as L, I, or F, or a non-polar residue such as A, as is observed inGallus gallus ALK4 (SEQ ID NO: 129). E40 in the human extracellulardomain is K in Gallus gallus ALK4, indicating that this site may betolerant of a wide variety of changes, including polar residues, such asE, D, K, R, H, S, T, P, G, Y, and probably a non-polar residue such asA. S15 in the human extracellular domain is D in Gallus gallus ALK4,indicating that a wide structural variation is tolerated at thisposition, with polar residues favored, such as S, T, R, E, K, H, G, P, Gand Y. E40 in the human extracellular domain is K in Gallus gallus ALK4,indicating that charged residues will be tolerated at this position,including D, R, K, H, as well as Q and N. R80 in the human extracellulardomain is K in Condylura cristata ALK4 (SEQ ID NO: 127), indicating thatbasic residues are tolerated at this position, including R, K, and H.Y77 in the human extracellular domain is F in Sus scrofa ALK4 (SEQ IDNO: 131), indicating that aromatic residues are tolerated at thisposition, including F, W, and Y. P93 in the human extracellular domainis relatively poorly conserved, appearing as S in Erinaceus europaeusALK4 (SEQ ID NO: 128) and N in Gallus gallus ALK4, thus essentially anyamino acid should be tolerated at this position.

Moreover, ALK4 proteins have been characterized in the art in terms ofstructural and functional characteristics, particularly with respect toligand binding [e.g., Harrison et al. (2003) J Biol Chem278(23):21129-21135; Romano et al. (2012) J Mol Model 18(8):3617-3625;and Calvanese et al. (2009) 15(3):175-183]. In addition to the teachingsherein, these references provide amply guidance for how to generate ALK4variants that retain one or more normal activities (e.g., ligand-bindingactivity).

For example, a defining structural motif known as a three-finger toxinfold is important for ligand binding by type I and type II receptors andis formed by conserved cysteine residues located at varying positionswithin the extracellular domain of each monomeric receptor [Greenwald etal. (1999) Nat Struct Biol 6:18-22; and Hinck (2012) FEBS Lett586:1860-1870]. Accordingly, the core ligand-binding domains of humanALK4, as demarcated by the outermost of these conserved cysteines,corresponds to positions 34-101 of SEQ ID NO: 100 (ALK4 precursor). Thestructurally less-ordered amino acids flanking these cysteine-demarcatedcore sequences can be truncated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33 residues at the N-terminus and/or by 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25residues at the C-terminus without necessarily altering ligand binding.Exemplary ALK4 extracellular domains for N-terminal and/or C-terminaltruncation include SEQ ID NOs: 101 and 105.

Accordingly, a general formula for an active portion (e.g., aligand-binding portion) of ALK4 comprises amino acids 34-101 withrespect to SEQ ID NO: 100. Therefore ALK4 polypeptides may, for example,comprise, consists essentially of, or consists of an amino acid sequencethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion ofALK4 beginning at a residue corresponding to any one of amino acids24-34 (e.g., beginning at any one of amino acids 24, 25, 26, 27, 28, 29,30, 31, 32, 33, or 34) of SEQ ID NO: 100 and ending at a positioncorresponding to any one amino acids 101-126 (e.g., ending at any one ofamino acids 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, or 126)of SEQ ID NO: 100. Other examples include constructs that begin at aposition from 24-34 (e.g., any one of positions 24, 25, 26, 27, 28, 29,30, 31, 32, 33, or 34), 25-34 (e.g., any one of positions 25, 26, 27,28, 29, 30, 31, 32, 33, or 34), or 26-34 (e.g., any one of positions 26,27, 28, 29, 30, 31, 32, 33, or 34) of SEQ ID NO: 100 and end at aposition from 101-126 (e.g., any one of positions 101, 102, 103, 104,105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, or 126), 102-126 (e.g., any one ofpositions 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113,114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, or 126),101-125 (e.g., any one of positions 101, 102, 103, 104, 105, 106, 107,108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,122, 123, 124, or 125), 101-124 (e.g., any one of positions 101, 102,103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,117, 118, 119, 120, 121, 122, 123, or 124), 101-121 (e.g., any one ofpositions 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, or 121), 111-126 (e.g., any oneof positions 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,123, 124, 125, or 126), 111-125 (e.g., any one of positions 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, or 125),111-124 (e.g., any one of positions 111, 112, 113, 114, 115, 116, 117,118, 119, 120, 121, 122, 123, or 124), 121-126 (e.g., any one ofpositions 121, 122, 123, 124, 125, or 126), 121-125 (e.g., any one ofpositions 121, 122, 123, 124, or 125), 121-124 (e.g., any one ofpositions 121, 122, 123, or 124), or 124-126 (e.g., any one of positions124, 125, or 126) of SEQ ID NO: 100. Variants within these ranges arealso contemplated, particularly those having at least 70%, 75%, 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identity to the corresponding portion of SEQ ID NO: 100.

The variations described herein may be combined in various ways. In someembodiments, ALK4 variants comprise no more than 1, 2, 5, 6, 7, 8, 9, 10or 15 conservative amino acid changes in the ligand-binding pocket.Sites outside the binding pocket, at which variability may beparticularly well tolerated, include the amino and carboxy termini ofthe extracellular domain (as noted above).

In certain embodiments, the disclosure relates to BMP/GDF antagoniststhat are heteromultimers comprising at least one ALK4 polypeptide, whichincludes fragments, functional variants, and modified forms thereof aswell as uses thereof (e.g., treating, preventing, or reducing theseverity of PAH or one or more complications of PAH). Preferably, ALK4polypeptides are soluble (e.g., an extracellular domain of ALK4). Insome embodiments, heteromultimers comprising an ALK4 polypeptide inhibit(e.g., Smad signaling) of one or more TGFβ superfamily ligands [e.g.,GDF11, GDF8, activin (activin A, activin B, activin AB, activin C,activin E) BMP6, GDF3, BMP10, and/or BMP9]. In some embodiments,heteromultimers comprising an ALK4 polypeptide bind to one or more TGFβsuperfamily ligands [e.g., GDF11, GDF8, activin (activin A, activin B,activin AB, activin C, activin E) BMP6, GDF3, BMP10, and/or BMP9]. Insome embodiments, heteromultimers comprise at least one ALK4 polypeptidethat is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 97%, 98%, 99%, 100% identical to amino acids 34-101 withrespect to SEQ ID NO: 100. In some embodiments, heteromultimers compriseat least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO: 100, 101, 104, 105,111, 113, 116, 117, 122, and 124. In some embodiments, heteromultimercomprise at least one ALK4 polypeptide that consist or consistessentially of at least one ALK4 polypeptide that is at least 70%, 75%,80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%,99%, or 100% identical to the amino acid sequence of SEQ ID NO: 100,101, 104, 105, 111, 113, 116, 117, 122, and 124.

In certain aspects, the present disclosure relates to heteromultimercomplexes comprising one or more ALK4 receptor polypeptides (e.g., SEQID Nos: 100, 101, 104, 105, 111, 113, 116, 117, 122, and 124 andvariants thereof) and one or more ActRIIB receptor polypeptides (e.g.,SEQ ID NOs: 1, 2, 3, 4, 5, 6, 58, 59, 60, 63, 64, 65, 66, 68, 69, 70,71, 73, 77, 78, 108, 110, 114, 115, 118, and 120 and land variantsthereof), which are generally referred to herein as “ALK4:ActRIIBheteromultimer complexes” or “ALK4:ActRIIB heteromultimers”, includinguses thereof (e.g., increasing an immune response in a patient in needthereof and treating cancer). Preferably, ALK4:ActRIIB heteromultimersare soluble [e.g., a heteromultimer complex comprises a soluble portion(domain) of an ALK4 receptor and a soluble portion (domain) of anActRIIB receptor]. In general, the extracellular domains of ALK4 andActRIIB correspond to soluble portion of these receptors. Therefore, insome embodiments, ALK4:ActRIIB heteromultimers comprise an extracellulardomain of an ALK4 receptor and an extracellular domain of an ActRIIBreceptor. In some embodiments, ALK4:ActRIIB heteromultimers inhibit(e.g., Smad signaling) of one or more TGFβ superfamily ligands [e.g.,GDF11, GDF8, activin (activin A, activin B, activin AB, activin C,activin E) BMP6, GDF3, BMP10, and/or BMP9]. In some embodiments,ALK4:ActRIIB heteromultimers bind to one or more TGFβ superfamilyligands [e.g., GDF11, GDF8, activin (activin A, activin B, activin AB,activin C, activin E) BMP6, GDF3, BMP10, and/or BMP9]. In someembodiments, ALK4:ActRIIB heteromultimers comprise at least one ALK4polypeptide that comprises, consists essentially of, or consists of asequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94% 95%, 97%, 98%, 99%, or 100% identical to the aminoacid sequence of SEQ ID NO: 100, 101, 104, 105, 111, 113, 116, 117, 122,and 124. In some embodiments, ALK4:ActRIIB heteromultimer complexes ofthe disclosure comprise at least one ALK4 polypeptide that comprises,consists essentially of, consists of a sequence that is at least 70%,75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 97%,98%, 99%, or 100% identical to a portion of ALK4 beginning at a residuecorresponding to any one of amino acids 24-34, 25-34, or 26-34 of SEQ IDNO: 100 and ending at a position from 101-126, 102-126, 101-125,101-124, 101-121, 111-126, 111-125, 111-124, 121-126, 121-125, 121-124,or 124-126 of SEQ ID NO: 100. In some embodiments, ALK4:ActRIIBheteromultimers comprise at least one ALK4 polypeptide that comprises,consists essentially of, consists of a sequence that is at least 70%,75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 97%,98%, 99%, or 100% identical to amino acids 34-101 with respect to SEQ IDNO: 100. In some embodiments, ALK4-ActRIIB heteromultimers comprise atleast one ActRIIB polypeptide that comprises, consists essentially of,consists of a sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 97%, 98%, 99%, or 100% identicalto the amino acid sequence of any one of SEQ ID NOs: 1, 2, 3, 4, 5, 6,58, 59, 60, 63, 64, 65, 66, 68, 69, 70, 71, 73, 77, 78, 108, 110, 114,115, 118, and 120. In some embodiments, ALK4:ActRIIB heteromultimercomplexes of the disclosure comprise at least one ActRIIB polypeptidethat comprises, consists essentially of, consists of a sequence that isat least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%95%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIB beginningat a residue corresponding to any one of amino acids 20-29, 20-24,21-24, 22-25, or 21-29 and end at a position from 109-134, 119-134,119-133, 129-134, or 129-133 of SEQ ID NO: 1. In some embodiments,ALK4:ActRIIB heteromultimers comprise at least one ActRIIB polypeptidethat comprises, consists essentially of, consists of a sequence that isat least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%95%, 97%, 98%, 99%, or 100% identical to amino acids 29-109 of SEQ IDNO: 1. In some embodiments, ALK4:ActRIIB heteromultimers comprise atleast one ActRIIB polypeptide that comprises, consists essentially of,consists of a sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94% 95%, 97%, 98%, 99%, or 100% identicalto amino acids 25-131 of SEQ ID NO: 1. In certain embodiments,ALK4:ActRIIB heteromultimer complexes of the disclosure comprise atleast one ActRIIB polypeptide wherein the position corresponding to L79of SEQ ID NO: 1 is not an acidic amino acid (i.e., not naturallyoccurring D or E amino acid residues or an artificial acidic amino acidresidue). ALK4:ActRIIB heteromultimers of the disclosure include, e.g.,heterodimers, heterotrimers, heterotetramers and further higher orderoligomeric structures. See, e.g., FIGS. 21-23. In certain preferredembodiments, heteromultimer complexes of the disclosure are ALK4:ActRIIBheterodimers.

In some embodiments, the present disclosure contemplates makingfunctional variants by modifying the structure of an ActRII and/or ALK4polypeptide for such purposes as enhancing therapeutic efficacy orstability (e.g., shelf-life and resistance to proteolytic degradation invivo). Variants can be produced by amino acid substitution, deletion,addition, or combinations thereof. For instance, it is reasonable toexpect that an isolated replacement of a leucine with an isoleucine orvaline, an aspartate with a glutamate, a threonine with a serine, or asimilar replacement of an amino acid with a structurally related aminoacid (e.g., conservative mutations) will not have a major effect on thebiological activity of the resulting molecule. Conservative replacementsare those that take place within a family of amino acids that arerelated in their side chains. Whether a change in the amino acidsequence of a polypeptide of the disclosure results in a functionalhomolog can be readily determined by assessing the ability of thevariant polypeptide to produce a response in cells in a fashion similarto the wild-type polypeptide, or to bind to one or more TGF-beta ligandsincluding, for example, BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6,BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8,GDF9b/BMP15, GDF11/BMP11, GDF15/MIC1, TGF-β1, TGF-β2, TGF-β3, activin A,activin B, activin C, activin E, activin AB, activin AC, nodal, glialcell-derived neurotrophic factor (GDNF), neurturin, artemin, persephin,MIS, and Lefty.

In certain embodiments, the present disclosure contemplates specificmutations of an ActRII and/or ALK4 polypeptide so as to alter theglycosylation of the polypeptide. Such mutations may be selected so asto introduce or eliminate one or more glycosylation sites, such asO-linked or N-linked glycosylation sites. Asparagine-linkedglycosylation recognition sites generally comprise a tripeptidesequence, asparagine-X-threonine or asparagine-X-serine (where “X” isany amino acid) which is specifically recognized by appropriate cellularglycosylation enzymes. The alteration may also be made by the additionof, or substitution by, one or more serine or threonine residues to thesequence of the polypeptide (for O-linked glycosylation sites). Avariety of amino acid substitutions or deletions at one or both of thefirst or third amino acid positions of a glycosylation recognition site(and/or amino acid deletion at the second position) results innon-glycosylation at the modified tripeptide sequence. Another means ofincreasing the number of carbohydrate moieties on a polypeptide is bychemical or enzymatic coupling of glycosides to the polypeptide.Depending on the coupling mode used, the sugar(s) may be attached to (a)arginine and histidine; (b) free carboxyl groups; (c) free sulfhydrylgroups such as those of cysteine; (d) free hydroxyl groups such as thoseof serine, threonine, or hydroxyproline; (e) aromatic residues such asthose of phenylalanine, tyrosine, or tryptophan; or (f) the amide groupof glutamine. Removal of one or more carbohydrate moieties present on apolypeptide may be accomplished chemically and/or enzymatically.Chemical deglycosylation may involve, for example, exposure of apolypeptide to the compound trifluoromethanesulfonic acid, or anequivalent compound. This treatment results in the cleavage of most orall sugars except the linking sugar (N-acetylglucosamine orN-acetylgalactosamine), while leaving the amino acid sequence intact.Enzymatic cleavage of carbohydrate moieties on polypeptides can beachieved by the use of a variety of endo- and exo-glycosidases asdescribed by Thotakura et al. [Meth. Enzymol. (1987) 138:350]. Thesequence of a polypeptide may be adjusted, as appropriate, depending onthe type of expression system used, as mammalian, yeast, insect, andplant cells may all introduce differing glycosylation patterns that canbe affected by the amino acid sequence of the peptide. In general,polypeptides of the present disclosure for use in humans may beexpressed in a mammalian cell line that provides proper glycosylation,such as HEK293 or CHO cell lines, although other mammalian expressioncell lines are expected to be useful as well.

The present disclosure further contemplates a method of generatingmutants, particularly sets of combinatorial mutants of an ActRII and/orALK4 polypeptide as well as truncation mutants. Pools of combinatorialmutants are especially useful for identifying functionally active (e.g.,GDF/BMP ligand binding) ActRII sequences. The purpose of screening suchcombinatorial libraries may be to generate, for example, polypeptidesvariants which have altered properties, such as altered pharmacokineticor altered ligand binding. A variety of screening assays are providedbelow, and such assays may be used to evaluate variants. For example,ActRII and/or ALK4 variants, and heteromultimers comprising the same,may be screened for ability to bind to one or more GDF/BMP ligands(e.g., BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6, BMP7, BMP8a, BMP8b,BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8, GDF9b/BMP15,GDF11/BMP11, GDF15/MIC1, TGF-β1, TGF-β2, TGF-β3, activin A, activin B,activin AB, activin AC, nodal, glial cell-derived neurotrophic factor(GDNF), neurturin, artemin, persephin, MIS, and Lefty), to preventbinding of a GDF/BMP ligand to an ActRII and/or ALK4 polypeptide, aswell as heteromultimers thereof, and/or to interfere with signalingcaused by an GDF/BMP ligand.

The activity of ActRII polypeptides, ALK4 polypeptides, and ALK4:ActRIIBheterodimers may also be tested in a cell-based or in vivo assay. Forexample, the effect of an ActRII polypeptide, ALK4 polypeptide, orALK4:ActRIIB heterodimer on the expression of genes involved in PHpathogenesis assessed. This may, as needed, be performed in the presenceof one or more recombinant ligand proteins (e.g., BMP2, BMP2/7, BMP3,BMP4, BMP4/7, BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF3, GDF5,GDF6/BMP13, GDF7, GDF8, GDF9b/BMP15, GDF11/BMP11, GDF15/MIC1, TGF-β1,TGF-β2, TGF-β3, activin A, activin B, activin C, activin E, activin AB,activin AC, nodal, glial cell-derived neurotrophic factor (GDNF),neurturin, artemin, persephin, MIS, and Lefty), and cells may betransfected so as to produce an ActRII polypeptide, ALK4 polypeptide, orALK4:ActRIIB heterodimer, and optionally, an GDF/BMP ligand. Likewise,an ActRII polypeptide, ALK4 polypeptide, or ALK4:ActRIIB heterodimer maybe administered to a mouse or other animal and effects on PHpathogenesis may be assessed using art-recognized methods. Similarly,the activity of an ActRII polypeptide, ALK4 polypeptide, or ALK4:ActRIIBheterodimer or variant thereof may be tested in blood cell precursorcells for any effect on growth of these cells, for example, by theassays as described herein and those of common knowledge in the art. ASMAD-responsive reporter gene may be used in such cell lines to monitoreffects on downstream signaling.

Combinatorial-derived variants can be generated which have increasedselectivity or generally increased potency relative to a referenceActRII polypeptide, ALK4 polypeptide, or ALK4:ActRIIB heterodimer. Suchvariants, when expressed from recombinant DNA constructs, can be used ingene therapy protocols. Likewise, mutagenesis can give rise to variantswhich have intracellular half-lives dramatically different than thecorresponding unmodified ActRII polypeptide, ALK4 polypeptide, orALK4:ActRIIB heterodimer. For example, the altered protein can berendered either more stable or less stable to proteolytic degradation orother cellular processes which result in destruction, or otherwiseinactivation, of an unmodified polypeptide. Such variants, and the geneswhich encode them, can be utilized to alter polypeptide complex levelsby modulating the half-life of the polypeptide. For instance, a shorthalf-life can give rise to more transient biological effects and, whenpart of an inducible expression system, can allow tighter control ofrecombinant polypeptide complex levels within the cell. In an Fc fusionprotein, mutations may be made in the linker (if any) and/or the Fcportion to alter the half-life of the ActRII polypeptide, ALK4polypeptide, or ALK4:ActRIIB heterodimer.

A combinatorial library may be produced by way of a degenerate libraryof genes encoding a library of polypeptides which each include at leasta portion of potential ActRII polypeptide, ALK4 polypeptide, orALK4:ActRIIB heterodimer sequences. For instance, a mixture of syntheticoligonucleotides can be enzymatically ligated into gene sequences suchthat the degenerate set of potential ActRII and/or or ALK4 encodingnucleotide sequences are expressible as individual polypeptides, oralternatively, as a set of larger fusion proteins (e.g., for phagedisplay).

There are many ways by which the library of potential homologs can begenerated from a degenerate oligonucleotide sequence. Chemical synthesisof a degenerate gene sequence can be carried out in an automatic DNAsynthesizer, and the synthetic genes can then be ligated into anappropriate vector for expression. The synthesis of degenerateoligonucleotides is well known in the art [Narang, S A (1983)Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc. 3rdCleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam: Elsevier pp273-289; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura etal. (1984) Science 198:1056; and Ike et al. (1983) Nucleic Acid Res.11:477]. Such techniques have been employed in the directed evolution ofother proteins [Scott et al., (1990) Science 249:386-390; Roberts et al.(1992) PNAS USA 89:2429-2433; Devlin et al. (1990) Science 249: 404-406;Cwirla et al., (1990) PNAS USA 87: 6378-6382; as well as U.S. Pat. Nos.5,223,409, 5,198,346, and 5,096,815].

Alternatively, other forms of mutagenesis can be utilized to generate acombinatorial library. For example, ActRII polypeptides, ALK4polypeptides, and ALK4:ActRIIB heterodimers of the disclosure can begenerated and isolated from a library by screening using, for example,alanine scanning mutagenesis [Ruf et al. (1994) Biochemistry33:1565-1572; Wang et al. (1994) J. Biol. Chem. 269:3095-3099; Balint etal. (1993) Gene 137:109-118; Grodberg et al. (1993) Eur. J. Biochem.218:597-601; Nagashima et al. (1993) J. Biol. Chem. 268:2888-2892;Lowman et al. (1991) Biochemistry 30:10832-10838; and Cunningham et al.(1989) Science 244:1081-1085], by linker scanning mutagenesis [Gustin etal. (1993) Virology 193:653-660; and Brown et al. (1992) Mol. Cell Biol.12:2644-2652; McKnight et al. (1982) Science 232:316], by saturationmutagenesis [Meyers et al., (1986) Science 232:613]; by PCR mutagenesis[Leung et al. (1989) Method Cell Mol Biol 1:11-19]; or by randommutagenesis, including chemical mutagenesis [Miller et al. (1992) AShort Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor,N.Y.; and Greener et al. (1994) Strategies in Mol Biol 7:32-34]. Linkerscanning mutagenesis, particularly in a combinatorial setting, is anattractive method for identifying truncated (bioactive) forms of ActRIIpolypeptides, ALK4 polypeptides, or ALK4:ActRIIB heterodimers.

A wide range of techniques are known in the art for screening geneproducts of combinatorial libraries made by point mutations andtruncations, and, for that matter, for screening cDNA libraries for geneproducts having a certain property. Such techniques will be generallyadaptable for rapid screening of the gene libraries generated by thecombinatorial mutagenesis of ActRII polypeptides. The most widely usedtechniques for screening large gene libraries typically comprise cloningthe gene library into replicable expression vectors, transformingappropriate cells with the resulting library of vectors, and expressingthe combinatorial genes under conditions in which detection of a desiredactivity facilitates relatively easy isolation of the vector encodingthe gene whose product was detected. Preferred assays include ligand(e.g., BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6, BMP7, BMP8a, BMP8b,BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8, GDF9b/BMP15,GDF11/BMP11, GDF15/MIC1, TGF-β1, TGF-β2, TGF-β3, activin A, activin B,activin C, activin E, activin AB, activin AC, nodal, glial cell-derivedneurotrophic factor (GDNF), neurturin, artemin, persephin, MIS, andLefty) binding assays and/or ligand-mediated cell signaling assays.

As will be recognized by one of skill in the art, most of the describedmutations, variants or modifications described herein may be made at thenucleic acid level or, in some cases, by post-translational modificationor chemical synthesis. Such techniques are well known in the art andsome of which are described herein. In part, the present disclosureidentifies functionally active portions (fragments) and variants ofActRII polypeptides, ALK4 polypeptides, or ALK4:ActRIIB heterodimesrthat can be used as guidance for generating and using other variantActRII polypeptides within the scope of the inventions described herein.

In certain embodiments, functionally active fragments of ActRIIpolypeptides, ALK4 polypeptides, and ALK4:ActRIIB heterodimesr of thepresent disclosure can be obtained by screening polypeptidesrecombinantly produced from the corresponding fragment of the nucleicacid encoding an ActRII and/or ALK4 polypeptides. In addition, fragmentscan be chemically synthesized using techniques known in the art such asconventional Merrifield solid phase f-Moc or t-Boc chemistry. Thefragments can be produced (recombinantly or by chemical synthesis) andtested to identify those peptidyl fragments that can function asantagonists (inhibitors) of ActRII and/or ALK4 receptors and/or one ormore ligands (e.g., BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6, BMP7,BMP8a, BMP8b, BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8,GDF9b/BMP15, GDF11/BMP11, GDF15/MIC1, TGF-β1, TGF-β2, TGF-β3, activin A,activin B, activin C, activin E, activin AB, activin AC, nodal, glialcell-derived neurotrophic factor (GDNF), neurturin, artemin, persephin,MIS, and Lefty).

In certain embodiments, ActRII polypeptide, ALK4 polypeptide, and/orALK4:ActRIIB heterodimer of the present disclosure may further comprisepost-translational modifications in addition to any that are naturallypresent in the ActRII polypeptide, ALK4 polypeptide, or ALK4:ActRIIBheterodimer. Such modifications include, but are not limited to,acetylation, carboxylation, glycosylation, phosphorylation, lipidation,and acylation. As a result, the ActRII polypeptide, ALK4 polypeptide, orALK4:ActRIIB heterodimer may contain non-amino acid elements, such aspolyethylene glycols, lipids, polysaccharide or monosaccharide, andphosphates. Effects of such non-amino acid elements on the functionalityof a ligand trap polypeptide may be tested as described herein for otherActRII, AKL4, and ALK4:ActRIIB variants. When a polypeptide of thedisclosure is produced in cells by cleaving a nascent form of thepolypeptide, post-translational processing may also be important forcorrect folding and/or function of the protein. Different cells (e.g.,CHO, HeLa, MDCK, 293, WI38, NIH-3T3 or HEK293) have specific cellularmachinery and characteristic mechanisms for such post-translationalactivities and may be chosen to ensure the correct modification andprocessing of the ActRII polypeptides.

In certain aspects, ActRII and ALK4 polypeptides of the presentdisclosure include fusion proteins having at least a portion (domain) ofan ActRII or ALK4 polypeptide and one or more heterologous portions(domains). Well-known examples of such fusion domains include, but arenot limited to, polyhistidine, Glu-Glu, glutathione S-transferase (GST),thioredoxin, protein A, protein G, an immunoglobulin heavy-chainconstant region (Fc), maltose binding protein (MBP), or human serumalbumin. A fusion domain may be selected so as to confer a desiredproperty. For example, some fusion domains are particularly useful forisolation of the fusion proteins by affinity chromatography. For thepurpose of affinity purification, relevant matrices for affinitychromatography, such as glutathione-, amylase-, and nickel- orcobalt-conjugated resins are used. Many of such matrices are availablein “kit” form, such as the Pharmacia GST purification system and theQIAexpress™ system (Qiagen) useful with (HIS₆) fusion partners. Asanother example, a fusion domain may be selected so as to facilitatedetection of the ActRII or ALK4 polypeptide. Examples of such detectiondomains include the various fluorescent proteins (e.g., GFP) as well as“epitope tags,” which are usually short peptide sequences for which aspecific antibody is available. Well-known epitope tags for whichspecific monoclonal antibodies are readily available include FLAG,influenza virus haemagglutinin (HA), and c-myc tags. In some cases, thefusion domains have a protease cleavage site, such as for Factor Xa orthrombin, which allows the relevant protease to partially digest thefusion proteins and thereby liberate the recombinant proteins therefrom.The liberated proteins can then be isolated from the fusion domain bysubsequent chromatographic separation. Other types of fusion domainsthat may be selected include multimerizing (e.g., dimerizing,tetramerizing) domains and functional domains (that confer an additionalbiological function) including, for example constant domains fromimmunoglobulins (e.g., Fc domains).

In certain aspects, ActRII and ALK4 polypeptides of the presentdisclosure contain one or more modifications that are capable of“stabilizing” the polypeptides. By “stabilizing” is meant anything thatincreases the in vitro half-life, serum half-life, regardless of whetherthis is because of decreased destruction, decreased clearance by thekidney, or other pharmacokinetic effect of the agent. For example, suchmodifications enhance the shelf-life of the polypeptides, enhancecirculatory half-life of the polypeptides, and/or reduce proteolyticdegradation of the polypeptides. Such stabilizing modifications include,but are not limited to, fusion proteins (including, for example, fusionproteins comprising an ActRII polypeptide (or ALK4 polypeptide) domainand a stabilizer domain), modifications of a glycosylation site(including, for example, addition of a glycosylation site to apolypeptide of the disclosure), and modifications of carbohydrate moiety(including, for example, removal of carbohydrate moieties from apolypeptide of the disclosure). As used herein, the term “stabilizerdomain” not only refers to a fusion domain (e.g., an immunoglobulin Fcdomain) as in the case of fusion proteins, but also includesnonproteinaceous modifications such as a carbohydrate moiety, ornonproteinaceous moiety, such as polyethylene glycol. In certainpreferred embodiments, an ActRII polypeptide (or ALK4 polypeptide) isfused with a heterologous domain that stabilizes the polypeptide (a“stabilizer” domain), preferably a heterologous domain that increasesstability of the polypeptide in vivo. Fusions with a constant domain ofan immunoglobulin (e.g., a Fc domain) are known to confer desirablepharmacokinetic properties on a wide range of proteins. Likewise,fusions to human serum albumin can confer desirable properties.

An example of a native amino acid sequence that may be used for the Fcportion of human IgG1 (G1Fc) is shown below (SEQ ID NO: 14). Dottedunderline indicates the hinge region, and solid underline indicatespositions with naturally occurring variants. In part, the disclosureprovides polypeptides comprising, consisting essential of, or consistingof amino acid sequences with 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity toSEQ ID NO: 14. Naturally occurring variants in G1Fc would include E134Dand M136L according to the numbering system used in SEQ ID NO: 14 (seeUniprot P01857).

(SEQ ID NO: 14) 1

 ELLGGPSVFL FPPKPKDTLM ISRTPEVTCV VVDVSHEDPE 51VKFNWYVDGV EVHNAKTKPR EEQYNSTYRV VSVLTVLHQD WLNGKEYKCK 101VSNKALPAPI EKTISKAKGQ PREPQVYTLP PSREEMTKNQ VSLTCLVKGF 151YPSDIAVEWE SNGQPENNYK TTPPVLDSDG SFFLYSKLTV DKSRWQQGNV 201FSCSVMHEAL HNHYTQKSLS LSPGK

Optionally, the IgG1 Fc domain has one or more mutations at residuessuch as Asp-265, lysine 322, and Asn-434. In certain cases, the mutantIgG1 Fc domain having one or more of these mutations (e.g., Asp-265mutation) has reduced ability of binding to the Fcγ receptor relative toa wild-type Fc domain. In other cases, the mutant Fc domain having oneor more of these mutations (e.g., Asn-434 mutation) has increasedability of binding to the MEW class I-related Fc-receptor (FcRN)relative to a wild-type IgG1 Fc domain.

An example of a native amino acid sequence that may be used for the Fcportion of human IgG2 (G2Fc) is shown below (SEQ ID NO: 15). Dottedunderline indicates the hinge region and double underline indicatespositions where there are data base conflicts in the sequence (accordingto UniProt P01859). In part, the disclosure provides polypeptidescomprising, consisting essential of, or consisting of amino acidsequences with 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 15.

(SEQ ID NO: 15) 1

 VAGPSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVQ 51FNWYVDGVEV HNAKTKPREE QFNSTFRVVS VLTVVHQDWL NGKEYKCKVS 101NKGLPAPIEK TISKTKGQPR EPQVYTLPPS REEMTKNQVS LTCLVKGFYP 151SDIAVEWESN GQPENNYKTT PPMLDSDGSF FLYSKLTVDK SRWQQGNVFS 201CSVMHEALHN HYTQKSLSLS PGK

Two examples of amino acid sequences that may be used for the Fc portionof human IgG3 (G3Fc) are shown below. The hinge region in G3Fc can be upto four times as long as in other Fc chains and contains three identical15-residue segments preceded by a similar 17-residue segment. The firstG3Fc sequence shown below (SEQ ID NO: 16) contains a short hinge regionconsisting of a single 15-residue segment, whereas the second G3Fcsequence (SEQ ID NO: 17) contains a full-length hinge region. In eachcase, dotted underline indicates the hinge region, and solid underlineindicates positions with naturally occurring variants according toUniProt P01859. In part, the disclosure provides polypeptidescomprising, consisting essential of, or consisting of amino acidsequences with 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NOs: 16and 17.

(SEQ ID NO: 16) 1

 

 GGPSVFLFPP KPKDTLMISR TPEVTCVVVD 51VSHEDPEVQF KWYVDGVEVH NAKTKPREEQ YNSTFRVVSV LTVLHQDWLN 101GKEYKCKVSN KALPAPIEKT ISKTKGQPRE PQVYTLPPSR EEMTKNQVSL 151TCLVKGFYPS DIAVEWESSG QPENNYNTTP PMLDSDGSFF LYSKLTVDKS 201RWQQGNIFSC SVMHEALHNR FTQKSLSLSP GK (SEQ ID NO: 17) 1

 

 

 

 

51

 

 SVFLFPPKPK DTLMISRTPE VTCVVVDVSH 101EDPEVQFKWY VDGVEVHNAK TKPREEQYNS TFRVVSVLTV LHQDWLNGKE 151YKCKVSNKAL PAPIEKTISK TKGQPREPQV YTLPPSREEM TKNQVSLTCL 201VKGFYPSDIA VEWESSGQPE NNYNTTPPML DSDGSFFLYS KLTVDKSRWQ 251QGNIFSCSVM HEALHNRFTQ KSLSLSPGK

Naturally occurring variants in G3Fc (for example, see Uniprot P01860)include E68Q, P76L, E79Q, Y81F, D97N, N100D, T124A, S169N, S169del,F221Y when converted to the numbering system used in SEQ ID NO: 16, andthe present disclosure provides fusion proteins comprising G3Fc domainscontaining one or more of these variations. In addition, the humanimmunoglobulin IgG3 gene (IGHG3) shows a structural polymorphismcharacterized by different hinge lengths [see Uniprot P01859].Specifically, variant WIS is lacking most of the V region and all of theCH1 region. It has an extra interchain disulfide bond at position 7 inaddition to the 11 normally present in the hinge region. Variant ZUClacks most of the V region, all of the CH1 region, and part of thehinge. Variant OMNI may represent an allelic form or another gamma chainsubclass. The present disclosure provides additional fusion proteinscomprising G3Fc domains containing one or more of these variants.

An example of a native amino acid sequence that may be used for the Fcportion of human IgG4 (G4Fc) is shown below (SEQ ID NO: 18). Dottedunderline indicates the hinge region. In part, the disclosure providespolypeptides comprising, consisting essential of, or consisting of aminoacid sequences with 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO:18.

(SEQ ID NO: 18) 1

 

 SVFLFPPKPK DTLMISRTPE VTCVVVDVSQ 51EDPEVQFNWY VDGVEVHNAK TKPREEQFNS TYRVVSVLTV LHQDWLNGKE 101YKCKVSNKGL PSSIEKTISK AKGQPREPQV YTLPPSQEEM TKNQVSLTCL 151VKGFYPSDIA VEWESNGQPE NNYKTTPPVL DSDGSFFLYS RLTVDKSRWQ 201EGNVFSCSVM HEALHNHYTQ KSLSLSLGK

A variety of engineered mutations in the Fc domain are presented hereinwith respect to the G1Fc sequence (SEQ ID NO: 14), and analogousmutations in G2Fc, G3Fc, and G4Fc can be derived from their alignmentwith G1Fc in FIG. 4. Due to unequal hinge lengths, analogous Fcpositions based on isotype alignment (FIG. 4) possess different aminoacid numbers in SEQ ID NOs: 14, 15, 16, 17, and 18. It can also beappreciated that a given amino acid position in an immunoglobulinsequence consisting of hinge, C_(H)2, and C_(H)3 regions (e.g., SEQ IDNOs: 14, 15, 16, 17, and 18) will be identified by a different numberthan the same position when numbering encompasses the entire IgG1heavy-chain constant domain (consisting of the C_(H)1, hinge, C_(H)2,and C_(H)3 regions) as in the Uniprot database. For example,correspondence between selected C_(H)3 positions in a human G1Fcsequence (SEQ ID NO: 14), the human IgG1 heavy chain constant domain(Uniprot P01857), and the human IgG1 heavy chain is as follows.

Correspondence of C_(H)3 Positions in Different Numbering Systems G1FcIgG1 heavy chain IgG1 heavy chain (Numbering begins constant domain (EUnumbering at first threonine (Numbering begins scheme of Kabat in hingeregion) at C_(H)1) et al., 1991*) Y127 Y232 Y349 S132 S237 S354 E134E239 E356 T144 T249 T366 L146 L251 L368 K170 K275 K392 D177 D282 D399Y185 Y290 Y407 K187 K292 K409 *Kabat et al. (eds) 1991; pp. 688-696 inSequences of Proteins of Immunological Interest, 5^(th) ed., Vol. 1,NIH, Bethesda, MD.

In certain aspects, the polypeptides disclosed herein may form proteincomplexes comprising at least one ALK4 polypeptide associated,covalently or non-covalently, with at least one ActRIIB polypeptide.Preferably, polypeptides disclosed herein form heterodimeric complexes,although higher order heteromultimeric complexes (heteromultimers) arealso included such as, but not limited to, heterotrimers,heterotetramers, and further oligomeric structures (see, e.g., FIG.21-23). In some embodiments, ALK4 and/or ActRIIB polypeptides compriseat least one multimerization domain. As disclosed herein, the term“multimerization domain” refers to an amino acid or sequence of aminoacids that promote covalent or non-covalent interaction between at leasta first polypeptide and at least a second polypeptide. Polypeptidesdisclosed herein may be joined covalently or non-covalently to amultimerization domain. Preferably, a multimerization domain promotesinteraction between a first polypeptide (e.g., an ALK4 polypeptide) anda second polypeptide (e.g., an ActRIIB polypeptide) to promoteheteromultimer formation (e.g., heterodimer formation), and optionallyhinders or otherwise disfavors homomultimer formation (e.g., homodimerformation), thereby increasing the yield of desired heteromultimer (see,e.g., FIG. 22).

Many methods known in the art can be used to generate ALK4:ActRIIBheteromultimers. For example, non-naturally occurring disulfide bondsmay be constructed by replacing on a first polypeptide (e.g., an ALK4polypeptide) a naturally occurring amino acid with a freethiol-containing residue, such as cysteine, such that the free thiolinteracts with another free thiol-containing residue on a secondpolypeptide (e.g., an ActRIIB polypeptide) such that a disulfide bond isformed between the first and second polypeptides. Additional examples ofinteractions to promote heteromultimer formation include, but are notlimited to, ionic interactions such as described in Kjaergaard et al.,WO2007147901; electrostatic steering effects such as described in Kannanet al., U.S. Pat. No. 8,592,562; coiled-coil interactions such asdescribed in Christensen et al., U.S. 20120302737; leucine zippers suchas described in Pack & Plueckthun, (1992) Biochemistry 31: 1579-1584;and helix-turn-helix motifs such as described in Pack et al., (1993)Bio/Technology 11: 1271-1277. Linkage of the various segments may beobtained via, e.g., covalent binding such as by chemical cross-linking,peptide linkers, disulfide bridges, etc., or affinity interactions suchas by avidin-biotin or leucine zipper technology.

In certain aspects, a multimerization domain may comprise one componentof an interaction pair. In some embodiments, the polypeptides disclosedherein may form protein complexes comprising a first polypeptidecovalently or non-covalently associated with a second polypeptide,wherein the first polypeptide comprises the amino acid sequence of anALK4 polypeptide and the amino acid sequence of a first member of aninteraction pair; and the second polypeptide comprises the amino acidsequence of an ActRIIB polypeptide and the amino acid sequence of asecond member of an interaction pair. The interaction pair may be anytwo polypeptide sequences that interact to form a complex, particularlya heterodimeric complex although operative embodiments may also employan interaction pair that can form a homodimeric complex. One member ofthe interaction pair may be fused to an ALK4 or ActRIIB polypeptide asdescribed herein, including for example, a polypeptide sequencecomprising, consisting essentially of, or consisting of an amino acidsequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to thesequence of any one of SEQ ID NOs: 2, 3, 5, 6, 101, and 103. Aninteraction pair may be selected to confer an improved property/activitysuch as increased serum half-life, or to act as an adaptor on to whichanother moiety is attached to provide an improved property/activity. Forexample, a polyethylene glycol moiety may be attached to one or bothcomponents of an interaction pair to provide an improvedproperty/activity such as improved serum half-life.

The first and second members of the interaction pair may be anasymmetric pair, meaning that the members of the pair preferentiallyassociate with each other rather than self-associate. Accordingly, firstand second members of an asymmetric interaction pair may associate toform a heterodimeric complex (see, e.g., FIG. 22). Alternatively, theinteraction pair may be unguided, meaning that the members of the pairmay associate with each other or self-associate without substantialpreference and thus may have the same or different amino acid sequences.Accordingly, first and second members of an unguided interaction pairmay associate to form a homodimer complex or a heterodimeric complex.Optionally, the first member of the interaction pair (e.g., anasymmetric pair or an unguided interaction pair) associates covalentlywith the second member of the interaction pair. Optionally, the firstmember of the interaction pair (e.g., an asymmetric pair or an unguidedinteraction pair) associates non-covalently with the second member ofthe interaction pair.

As specific examples, the present disclosure provides fusion proteinscomprising ALK4 or ActRIIB fused to a polypeptide comprising a constantdomain of an immunoglobulin, such as a CH1, CH2, or CH3 domain derivedfrom human IgG1, IgG2, IgG3, and/or IgG4 that has been modified topromote heteromultimer formation. A problem that arises in large-scaleproduction of asymmetric immunoglobulin-based proteins from a singlecell line is known as the “chain association issue”. As confrontedprominently in the production of bispecific antibodies, the chainassociation issue concerns the challenge of efficiently producing adesired multi-chain protein from among the multiple combinations thatinherently result when different heavy chains and/or light chains areproduced in a single cell line [Klein et al (2012) mAbs 4:653-663]. Thisproblem is most acute when two different heavy chains and two differentlight chains are produced in the same cell, in which case there are atotal of 16 possible chain combinations (although some of these areidentical) when only one is typically desired. Nevertheless, the sameprinciple accounts for diminished yield of a desired multi-chain fusionprotein that incorporates only two different (asymmetric) heavy chains.

Various methods are known in the art that increase desired pairing ofFc-containing fusion polypeptide chains in a single cell line to producea preferred asymmetric fusion protein at acceptable yields [Klein et al(2012) mAbs 4:653-663; and Spiess et al (2015) Molecular Immunology67(2A): 95-106]. Methods to obtain desired pairing of Fc-containingchains include, but are not limited to, charge-based pairing(electrostatic steering), “knobs-into-holes” steric pairing, SEEDbodypairing, and leucine zipper-based pairing [Ridgway et al (1996) ProteinEng 9:617-621; Merchant et al (1998) Nat Biotech 16:677-681; Davis et al(2010) Protein Eng Des Sel 23:195-202; Gunasekaran et al (2010);285:19637-19646; Wranik et al (2012) J Biol Chem 287:43331-43339; U.S.Pat. No. 5,932,448; WO 1993/011162; WO 2009/089004, and WO 2011/034605].As described herein, these methods may be used to generateALK4-Fc:ActRIIB-Fc heteromultimer complexes. See, e.g., FIG. 23.

ALK4:ActRIIB heteromultimers and method of making such heteromultimershave been previously disclosed. See, for example, WO 2016/164497, theentire teachings of which are incorporated by reference herein.

It is understood that different elements of the fusion proteins (e.g.,immunoglobulin Fc fusion proteins) may be arranged in any manner that isconsistent with desired functionality. For example, an ActRIIpolypeptide (or ALK4 polypeptide) domain may be placed C-terminal to aheterologous domain, or alternatively, a heterologous domain may beplaced C-terminal to an ActRII polypeptide (or ALK4 polypeptide) domain.The ActRII polypeptide (or ALK4 polypeptide) domain and the heterologousdomain need not be adjacent in a fusion protein, and additional domainsor amino acid sequences may be included C- or N-terminal to eitherdomain or between the domains.

For example, an ActRII (or ALK4) receptor fusion protein may comprise anamino acid sequence as set forth in the formula A-B-C. The B portioncorresponds to an ActRII (or ALK4) polypeptide domain. The A and Cportions may be independently zero, one, or more than one amino acid,and both the A and C portions when present are heterologous to B. The Aand/or C portions may be attached to the B portion via a linkersequence. A linker may be rich in glycine (e.g., 2-10, 2-5, 2-4, 2-3glycine residues) or glycine and proline residues and may, for example,contain a single sequence of threonine/serine and glycines or repeatingsequences of threonine/serine and/or glycines, e.g., GGG (SEQ ID NO:19), GGGG (SEQ ID NO: 20), TGGGG (SEQ ID NO: 21), SGGGG (SEQ ID NO: 22),TGGG (SEQ ID NO: 23), SGGG (SEQ ID NO: 24), or GGGGS (SEQ ID NO: 25)singlets, or repeats. In certain embodiments, an ActRII (or ALK4) fusionprotein comprises an amino acid sequence as set forth in the formulaA-B-C, wherein A is a leader (signal) sequence, B consists of an ActRII(or ALK4) polypeptide domain, and C is a polypeptide portion thatenhances one or more of in vivo stability, in vivo half-life,uptake/administration, tissue localization or distribution, formation ofprotein complexes, and/or purification. In certain embodiments, anActRII (or ALK4) fusion protein comprises an amino acid sequence as setforth in the formula A-B-C, wherein A is a TPA leader sequence, Bconsists of an ActRII (or ALK4) receptor polypeptide domain, and C is animmunoglobulin Fc domain. Preferred fusion proteins comprise the aminoacid sequence set forth in any one of SEQ ID NOs: 32, 36, 39, 40, 42,45, 46, 48, 69, 74, 77, 78, 108, 110, 111, 113, 114, 115, 116, 117, 118,120, 122, and 124.

In preferred embodiments, ActRII polypeptides, ALK4 polypeptides, andALK4:ActRIIB heteromultimers to be used in accordance with the methodsdescribed herein are isolated polypeptides. As used herein, an isolatedprotein or polypeptide is one which has been separated from a componentof its natural environment. In some embodiments, a polypeptide of thedisclosure is purified to greater than 95%, 96%, 97%, 98%, or 99% purityas determined by, for example, electrophoretic (e.g., SDS-PAGE,isoelectric focusing (IEF), capillary electrophoresis) orchromatographic (e.g., ion exchange or reverse phase HPLC). Methods forassessment of purity are well known in the art [see, e.g., Flatman etal., (2007) J. Chromatogr. B 848:79-87]. In some embodiments, ActRIIpolypeptides, ALK4 polypeptides, and ALK4:ActRIIB heteromultimers to beused in accordance with the methods described herein are recombinantpolypeptides.

ActRII polypeptides, ALK4 polypeptides, and ALK4:ActRIIB heteromultimersof the disclosure can be produced by a variety of art-known techniques.For example, polypeptides of the disclosure can be synthesized usingstandard protein chemistry techniques such as those described inBodansky, M. Principles of Peptide Synthesis, Springer Verlag, Berlin(1993) and Grant G. A. (ed.), Synthetic Peptides: A User's Guide, W. H.Freeman and Company, New York (1992). In addition, automated peptidesynthesizers are commercially available (e.g., Advanced ChemTech Model396; Milligen/Biosearch 9600). Alternatively, the polypeptides of thedisclosure, including fragments or variants thereof, may berecombinantly produced using various expression systems [e.g., E. coli,Chinese Hamster Ovary (CHO) cells, COS cells, baculovirus] as is wellknown in the art. In a further embodiment, the modified or unmodifiedpolypeptides of the disclosure may be produced by digestion ofrecombinantly produced full-length ActRII polypeptides by using, forexample, a protease, e.g., trypsin, thermolysin, chymotrypsin, pepsin,or paired basic amino acid converting enzyme (PACE). Computer analysis(using commercially available software, e.g., MacVector, Omega, PCGene,Molecular Simulation, Inc.) can be used to identify proteolytic cleavagesites. Alternatively, such polypeptides may be produced fromrecombinantly generated full-length ActRII or ALK4 polypeptides usingchemical cleavage (e.g., cyanogen bromide, hydroxylamine, etc.).

3. Nucleic Acids Encoding ActRII and ALK4 Polypeptides and VariantsThereof

In certain embodiments, the present disclosure provides isolated and/orrecombinant nucleic acids encoding ActRII and/or ALK4 polypeptides(including fragments, functional variants, and fusion proteins thereof).For example, SEQ ID NO: 7 encodes a naturally occurring human ActRIIBprecursor polypeptide (the R64 variant described above), while SEQ IDNO: 8 encodes the processed extracellular domain of ActRIIB (the R64variant described above). The subject nucleic acids may besingle-stranded or double-stranded. Such nucleic acids may be DNA or RNAmolecules. These nucleic acids may be used, for example, in methods formaking ActRII-based ligand trap polypeptides as described herein.

As used herein, isolated nucleic acid(s) refers to a nucleic acidmolecule that has been separated from a component of its naturalenvironment. An isolated nucleic acid includes a nucleic acid moleculecontained in cells that ordinarily contain the nucleic acid molecule,but the nucleic acid molecule is present extrachromosomally or at achromosomal location that is different from its natural chromosomallocation.

In certain embodiments, nucleic acids encoding ActRII or ALK4polypeptides of the disclosure are understood to include nucleic acidsthat are variants of any one of SEQ ID NOs: 7, 8, 12, 13, 37, 43, 49,70, 71, 72, 73, 75, 76, 80, 81, 82, 83, 84, 102, 103, 106, 107, 109,112, 119, 121, 123, and 135. Variant nucleotide sequences includesequences that differ by one or more nucleotide substitutions,additions, or deletions including allelic variants, and therefore, willinclude coding sequence that differ from the nucleotide sequencedesignated in any one of SEQ ID NOs: 7, 8, 12, 13, 37, 43, 49, 70, 71,72, 73, 75, 76, 80, 81, 82, 83, 84, 102, 103, 106, 107, 109, 112, 119,121, 123, and 135.

In certain embodiments, ActRII or ALK4 polypeptides of the disclosureare encoded by isolated and/or recombinant nucleic acid sequences thatare at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97%,98%, 99%, or 100% identical to any one of SEQ ID NOs: 7, 8, 12, 13, 37,43, 49, 70, 71, 72, 73, 75, 76, 80, 81, 82, 83, 84, 102, 103, 106, 107,109, 112, 119, 121, 123, and 135. One of ordinary skill in the art willappreciate that nucleic acid sequences that are at least 70%, 75%, 80%,85%, 90%, 91%, 92%, 93%, 94% 95%, 96%, 97%, 98%, 99%, or 100% identicalto the sequences complementary to SEQ ID NOs: 7, 8, 12, 13, 37, 43, 49,70, 71, 72, 73, 75, 76, 80, 81, 82, 83, 84, 102, 103, 106, 107, 109,112, 119, 121, 123, and 135, and variants thereof, are also within thescope of the present disclosure. In further embodiments, the nucleicacid sequences of the disclosure can be isolated, recombinant, and/orfused with a heterologous nucleotide sequence, or in a DNA library.

In other embodiments, nucleic acids of the present disclosure alsoinclude nucleotide sequences that hybridize under highly stringentconditions to the nucleotide sequence designated in SEQ ID NOs: 7, 8,12, 13, 37, 43, 49, 70, 71, 72, 73, 75, 76, 80, 81, 82, 83, 84, 102,103, 106, 107, 109, 112, 119, 121, 123, and 135, complement sequences ofSEQ ID NOs: 7, 8, 12, 13, 37, 43, 49, 70, 71, 72, 73, 75, 76, 80, 81,82, 83, 84, 102, 103, 106, 107, 109, 112, 119, 121, 123, and 135, orfragments thereof. As discussed above, one of ordinary skill in the artwill understand readily that appropriate stringency conditions whichpromote DNA hybridization can be varied. One of ordinary skill in theart will understand readily that appropriate stringency conditions whichpromote DNA hybridization can be varied. For example, one could performthe hybridization at 6.0×sodium chloride/sodium citrate (SSC) at about45° C., followed by a wash of 2.0×SSC at 50° C. For example, the saltconcentration in the wash step can be selected from a low stringency ofabout 2.0×SSC at 50° C. to a high stringency of about 0.2×SSC at 50° C.In addition, the temperature in the wash step can be increased from lowstringency conditions at room temperature, about 22° C., to highstringency conditions at about 65° C. Both temperature and salt may bevaried, or temperature or salt concentration may be held constant whilethe other variable is changed. In one embodiment, the disclosureprovides nucleic acids which hybridize under low stringency conditionsof 6×SSC at room temperature followed by a wash at 2×SSC at roomtemperature.

Isolated nucleic acids which differ from the nucleic acids as set forthin SEQ ID NOs: 7, 8, 12, 13, 37, 43, 49, 70, 71, 72, 73, 75, 76, 80, 81,82, 83, 84, 102, 103, 106, 107, 109, 112, 119, 121, 123, and 135 todegeneracy in the genetic code are also within the scope of thedisclosure.

For example, a number of amino acids are designated by more than onetriplet. Codons that specify the same amino acid, or synonyms (forexample, CAU and CAC are synonyms for histidine) may result in “silent”mutations which do not affect the amino acid sequence of the protein.However, it is expected that DNA sequence polymorphisms that do lead tochanges in the amino acid sequences of the subject proteins will existamong mammalian cells. One skilled in the art will appreciate that thesevariations in one or more nucleotides (up to about 3-5% of thenucleotides) of the nucleic acids encoding a particular protein mayexist among individuals of a given species due to natural allelicvariation. Any and all such nucleotide variations and resulting aminoacid polymorphisms are within the scope of this disclosure.

In certain embodiments, the recombinant nucleic acids of the presentdisclosure may be operably linked to one or more regulatory nucleotidesequences in an expression construct. Regulatory nucleotide sequenceswill generally be appropriate to the host cell used for expression.Numerous types of appropriate expression vectors and suitable regulatorysequences are known in the art and can be used in a variety of hostcells. Typically, one or more regulatory nucleotide sequences mayinclude, but are not limited to, promoter sequences, leader or signalsequences, ribosomal binding sites, transcriptional start andtermination sequences, translational start and termination sequences,and enhancer or activator sequences. Constitutive or inducible promotersas known in the art are contemplated by the disclosure. The promotersmay be either naturally occurring promoters, or hybrid promoters thatcombine elements of more than one promoter. An expression construct maybe present in a cell on an episome, such as a plasmid, or the expressionconstruct may be inserted in a chromosome. In some embodiments, theexpression vector contains a selectable marker gene to allow theselection of transformed host cells. Selectable marker genes are wellknown in the art and can vary with the host cell used.

In certain aspects, the subject nucleic acid disclosed herein isprovided in an expression vector comprising a nucleotide sequenceencoding an ActRII and/or ALK4 polypeptide and operably linked to atleast one regulatory sequence. Regulatory sequences are art-recognizedand are selected to direct expression of the ActRII and/or ALK4polypeptide. Accordingly, the term regulatory sequence includespromoters, enhancers, and other expression control elements. Exemplaryregulatory sequences are described in Goeddel; Gene ExpressionTechnology: Methods in Enzymology, Academic Press, San Diego, Calif.(1990). For instance, any of a wide variety of expression controlsequences that control the expression of a DNA sequence when operativelylinked to it may be used in these vectors to express DNA sequencesencoding an ActRII and/or ALK4 polypeptide. Such useful expressioncontrol sequences, include, for example, the early and late promoters ofSV40, tet promoter, adenovirus or cytomegalovirus immediate earlypromoter, RSV promoters, the lac system, the trp system, the TAC or TRCsystem, T7 promoter whose expression is directed by T7 RNA polymerase,the major operator and promoter regions of phage lambda, the controlregions for fd coat protein, the promoter for 3-phosphoglycerate kinaseor other glycolytic enzymes, the promoters of acid phosphatase, e.g.,Pho5, the promoters of the yeast a-mating factors, the polyhedronpromoter of the baculovirus system and other sequences known to controlthe expression of genes of prokaryotic or eukaryotic cells or theirviruses, and various combinations thereof. It should be understood thatthe design of the expression vector may depend on such factors as thechoice of the host cell to be transformed and/or the type of proteindesired to be expressed. Moreover, the vector's copy number, the abilityto control that copy number and the expression of any other proteinencoded by the vector, such as antibiotic markers, should also beconsidered.

A recombinant nucleic acid of the present disclosure can be produced byligating the cloned gene, or a portion thereof, into a vector suitablefor expression in either prokaryotic cells, eukaryotic cells (yeast,avian, insect or mammalian), or both. Expression vehicles for productionof a recombinant ActRII and/or ALK4 polypeptide include plasmids andother vectors. For instance, suitable vectors include plasmids of thefollowing types: pBR322-derived plasmids, pEMBL-derived plasmids,pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmidsfor expression in prokaryotic cells, such as E. coli.

Some mammalian expression vectors contain both prokaryotic sequences tofacilitate the propagation of the vector in bacteria, and one or moreeukaryotic transcription units that are expressed in eukaryotic cells.The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2,pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples ofmammalian expression vectors suitable for transfection of eukaryoticcells. Some of these vectors are modified with sequences from bacterialplasmids, such as pBR322, to facilitate replication and drug resistanceselection in both prokaryotic and eukaryotic cells. Alternatively,derivatives of viruses such as the bovine papilloma virus (BPV-1), orEpstein-Barr virus (pHEBo, pREP-derived and p205) can be used fortransient expression of proteins in eukaryotic cells. Examples of otherviral (including retroviral) expression systems can be found below inthe description of gene therapy delivery systems. The various methodsemployed in the preparation of the plasmids and in transformation ofhost organisms are well known in the art. For other suitable expressionsystems for both prokaryotic and eukaryotic cells, as well as generalrecombinant procedures, e.g., Molecular Cloning A Laboratory Manual, 3rdEd., ed. by Sambrook, Fritsch and Maniatis (Cold Spring HarborLaboratory Press, 2001). In some instances, it may be desirable toexpress the recombinant polypeptides by the use of a baculovirusexpression system. Examples of such baculovirus expression systemsinclude pVL-derived vectors (such as pVL1392, pVL1393 and pVL941),pAcUW-derived vectors (such as pAcUW1), and pBlueBac-derived vectors(such as the β-gal containing pBlueBac III).

In a preferred embodiment, a vector will be designed for production ofthe subject ActRII and/or ALK4 polypeptides in CHO cells, such as aPcmv-Script vector (Stratagene, La Jolla, Calif.), pcDNA4 vectors(Invitrogen, Carlsbad, Calif.) and pCI-neo vectors (Promega, Madison,Wisc.). As will be apparent, the subject gene constructs can be used tocause expression of the subject ActRII polypeptides in cells propagatedin culture, e.g., to produce proteins, including fusion proteins orvariant proteins, for purification.

This disclosure also pertains to a host cell transfected with arecombinant gene including a coding sequence for one or more of thesubject ActRII and/or ALK4 polypeptides. The host cell may be anyprokaryotic or eukaryotic cell. For example, an ActRII and/or ALK4polypeptide of the disclosure may be expressed in bacterial cells suchas E. coli, insect cells (e.g., using a baculovirus expression system),yeast, or mammalian cells [e.g. a Chinese hamster ovary (CHO) cellline]. Other suitable host cells are known to those skilled in the art.

Accordingly, the present disclosure further pertains to methods ofproducing the subject ActRII and/or ALK4 polypeptides. For example, ahost cell transfected with an expression vector encoding an ActRIIand/or ALK4 polypeptide can be cultured under appropriate conditions toallow expression of the ActRII and/or ALK4 polypeptide to occur. Thepolypeptide may be secreted and isolated from a mixture of cells andmedium containing the polypeptide. Alternatively, the ActRII and/or ALK4polypeptide may be retained cytoplasmically or in a membrane fractionand the cells harvested, lysed and the protein isolated. A cell cultureincludes host cells, media and other byproducts. Suitable media for cellculture are well known in the art. The subject polypeptides can beisolated from cell culture medium, host cells, or both, using techniquesknown in the art for purifying proteins, including ion-exchangechromatography, gel filtration chromatography, ultrafiltration,electrophoresis, immunoaffinity purification with antibodies specificfor particular epitopes of the ActRII and/or ALK4 polypeptides, andaffinity purification with an agent that binds to a domain fused to theActRII polypeptide (e.g., a protein A column may be used to purify anActRII-Fc and/or ALK4-Fc fusion proteins). In some embodiments, theActRII and/or ALK4 polypeptide is a fusion protein containing a domainwhich facilitates its purification.

In some embodiments, purification is achieved by a series of columnchromatography steps, including, for example, three or more of thefollowing, in any order: protein A chromatography, Q sepharosechromatography, phenylsepharose chromatography, size exclusionchromatography, and cation exchange chromatography. The purificationcould be completed with viral filtration and buffer exchange. An ActRIIand/or ALK4 protein may be purified to a purityof >90%, >95%, >96%, >98%, or >99% as determined by size exclusionchromatography and >90%, >95%, >96%, >98%, or >99% as determined by SDSPAGE. The target level of purity should be one that is sufficient toachieve desirable results in mammalian systems, particularly non-humanprimates, rodents (mice), and humans.

In another embodiment, a fusion gene coding for a purification leadersequence, such as a poly-(His)/enterokinase cleavage site sequence atthe N-terminus of the desired portion of the recombinant ActRII and/orALK4 polypeptide, can allow purification of the expressed fusion proteinby affinity chromatography using a Ni²⁺ metal resin. The purificationleader sequence can then be subsequently removed by treatment withenterokinase to provide the purified ActRII and/or ALK4 polypeptide.See, e.g., Hochuli et al. (1987) 1 Chromatography 411:177; and Janknechtet al. (1991) PNAS USA 88:8972.

Techniques for making fusion genes are well known. Essentially, thejoining of various DNA fragments coding for different polypeptidesequences is performed in accordance with conventional techniques,employing blunt-ended or stagger-ended termini for ligation, restrictionenzyme digestion to provide for appropriate termini, filling-in ofcohesive ends as appropriate, alkaline phosphatase treatment to avoidundesirable joining, and enzymatic ligation. In another embodiment, thefusion gene can be synthesized by conventional techniques includingautomated DNA synthesizers. Alternatively, PCR amplification of genefragments can be carried out using anchor primers which give rise tocomplementary overhangs between two consecutive gene fragments which cansubsequently be annealed to generate a chimeric gene sequence. See,e.g., Current Protocols in Molecular Biology, eds. Ausubel et al., JohnWiley & Sons: 1992.

4. Antibody Antagonists

In certain aspects, a GDF/BMP antagonist to be used in accordance withthe methods and uses disclosed herein is an antibody (GDF/BMP antagonistantibody), or combination of antibodies. A GDF/BMP antagonist antibody,or combination of antibodies, may bind to, for example, one or moreActRII ligands (e.g., activin, GDF8, GDF11, BMP6, BMP15, BMP10, and/orGDF3), ActRII receptor (ActRIIA and/or ActRIIB), type I receptor (ALK4,ALK5, and/or ALK7) and/or co-receptor. As described herein, GDF/BMPantagonist antibodies may be used, alone or in combination with one ormore supportive therapies or active agents, to treat, prevent, or reducethe progression rate and/or severity of pulmonary hypertension (PH),particularly treating, preventing or reducing the progression rateand/or severity of one or more PH-associated complications.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least activin (e.g., activinA, activin B, activin C, activin E, activin AB, activin AC, activin BC,activin AE, and/or activin BE). Therefore, in some embodiments, aGDF/BMP antagonist antibody, or combination of antibodies, binds to atleast activin. As used herein, an activin antibody (or anti-activinantibody) generally refers to an antibody that binds to activin withsufficient affinity such that the antibody is useful as a diagnosticand/or therapeutic agent in targeting activin. In certain embodiments,the extent of binding of an activin antibody to an unrelated,non-activin protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%,2%, or less than about 1% of the binding of the antibody to activin asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments,an activin antibody binds to an epitope of activin that is conservedamong activin from different species. In certain preferred embodiments,an anti-activin antibody binds to human activin. In some embodiments, anactivin antibody may inhibit activin from binding to a type I and/ortype II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) andthus inhibit activin-mediated signaling (e.g., Smad signaling). In someembodiments, an activin antibody may inhibit activin from binding to anActRII co-receptor and thus inhibit activin-mediated signaling (e.g.,Smad signaling). It should be noted that activin A has similar sequencehomology to activin B and therefore antibodies that bind to activin A,in some instances, may also bind to and/or inhibit activin B, which alsoapplies to anti-activin B antibodies. In some embodiments, thedisclosure relates to a multispecific antibody (e.g., bi-specificantibody), and uses thereof, that binds to activin and further binds to,for example, one or more additional GDF/BMP ligands [e.g., GDF11, GDF8,GDF3, BMP15, BMP10, and BMP6], one or more type I receptor and/or typeII receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/orone or more co-receptors. In some embodiments, a multispecific antibodythat binds to activin does not bind or does not substantially bind toBMP9 (e.g., binds to BMP9 with a K_(D) of greater than 1×10⁻⁷ M or hasrelatively modest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). Insome embodiments, a multispecific antibody that binds to activin doesnot bind or does not substantially bind to activin A (e.g., binds toactivin A with a K_(D) of greater than 1×10⁻⁷ M or has relatively modestbinding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). In some embodiments, thedisclosure relates to combinations of antibodies, and uses thereof,wherein the combination of antibodies comprises an activin antibody andone or more additional antibodies that bind to, for example, one or moreadditional GDF/BMP superfamily ligands [e.g., GDF8, GDF11, GDF3, BMP6,and BMP15], one or more type I receptor and/or type II receptors (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a combination of antibodies thatcomprises an activin antibody does not comprise a BMP9 antibody. In someembodiments, a combination of antibodies that comprises an activinantibody does not comprise an activin A antibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least activin B. Therefore,in some embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least activin B. As used herein, an activin Bantibody (or anti-activin B antibody) generally refers to an antibodythat binds to activin B with sufficient affinity such that the antibodyis useful as a diagnostic and/or therapeutic agent in targeting activinB. In certain embodiments, the extent of binding of an activin Bantibody to an unrelated, non-activin B protein is less than about 10%,9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding ofthe antibody to activin as measured, for example, by a radioimmunoassay(RIA), Biacore, or other protein interaction or binding affinity assay.In certain embodiments, an activin B antibody binds to an epitope ofactivin B that is conserved among activin B from different species. Incertain preferred embodiments, an anti-activin B antibody binds to humanactivin B. In some embodiments, an activin B antibody may inhibitactivin B from binding to a type I and/or type II receptor (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit activinB-mediated signaling (e.g., Smad signaling). In some embodiments, anactivin B antibody may inhibit activin B from binding to a co-receptorand thus inhibit activin B-mediated signaling (e.g., Smad signaling). Itshould be noted that activin B has similar sequence homology to activinA and therefore antibodies that bind to activin B, in some instances,may also bind to and/or inhibit activin A. In some embodiments, thedisclosure relates to a multispecific antibody (e.g., bi-specificantibody), and uses thereof, that binds to activin B and further bindsto, for example, one or more additional GDF/BMP ligands [e.g., GDF11,GDF8, GDF3, BMP15, BMP10, and BMP6], one or more type I receptor and/ortype II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7),and/or one or more co-receptors. In some embodiments, a multispecificantibody that binds to activin B does not bind or does not substantiallybind to BMP9 (e.g., binds to BMP9 with a K_(D) of greater than 1×10⁻⁷ Mor has relatively modest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M).In some embodiments, a multispecific antibody that binds to activin Bdoes not bind or does not substantially bind to activin A (e.g., bindsto activin A with a K_(D) of greater than 1×10⁻⁷ M or has relativelymodest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). In someembodiments, the disclosure relates to combinations of antibodies, anduses thereof, wherein the combination of antibodies comprises an activinB antibody and one or more additional antibodies that bind to, forexample, one or more additional GDF/BMP ligands [e.g., GDF8, GDF11,GDF3, BMP6, BMP10, and BMP15], one or more type I receptor and/or typeII receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/orone or more co-receptors. In some embodiments, a combination ofantibodies that comprises an activin B antibody does not comprise a BMP9antibody. In some embodiments, a combination of antibodies thatcomprises an activin B antibody does not comprise an activin A antibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least GDF8. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least GDF8. As used herein, a GDF8 antibody (oranti-GDF8 antibody) generally refers to an antibody that binds to GDF8with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting GDF8. In certainembodiments, the extent of binding of a GDF8 antibody to an unrelated,non-GDF8 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%,or less than about 1% of the binding of the antibody to GDF8 asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments, aGDF8 antibody binds to an epitope of GDF8 that is conserved among GDF8from different species. In certain preferred embodiments, an anti-GDF8antibody binds to human GDF8. In some embodiments, a GDF8 antibody mayinhibit GDF8 from binding to a type I and/or type II receptor (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibitGDF8-mediated signaling (e.g., Smad signaling). In some embodiments, aGDF8 antibody may inhibit GDF8 from binding to a co-receptor and thusinhibit GDF8-mediated signaling (e.g., Smad signaling). It should benoted that GDF8 has high sequence homology to GDF11 and thereforeantibodies that bind to GDF8, in some instances, may also bind to and/orinhibit GDF11. In some embodiments, the disclosure relates to amultispecific antibody (e.g., bi-specific antibody), and uses thereof,that binds to GDF8 and further binds to, for example, one or moreadditional GDF/BMP ligands [e.g., activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin BC, activin AE,activin BE), GDF11, GDF3, BMP15, BMP10, and BMP6], one or more type Ireceptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5,and/or ALK7), and/or one or more co-receptors. In some embodiments, amultispecific antibody that binds to GDF8 does not bind or does notsubstantially bind to BMP9 (e.g., binds to BMP9 with a K_(D) of greaterthan 1×10⁻⁷M or has relatively modest binding, e.g., about 1×10⁻⁸ M orabout 1×10⁻⁹M). In some embodiments, a multispecific antibody that bindsto GDF8 does not bind or does not substantially bind to activin A (e.g.,binds to activin A with a K_(D) of greater than 1×10⁻⁷M or hasrelatively modest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). Insome embodiments, the disclosure relates to combinations of antibodies,and uses thereof, wherein the combination of antibodies comprises a GDF8antibody and one or more additional antibodies that bind to, forexample, one or more additional GDF/BMP ligands [e.g., activin (e.g.,activin A, activin B, activin C, activin E, activin AB, activin AC,activin BC, activin AE, activin BE), GDF11, GDF3, BMP6, BMP10, andBMP15], one or more type I receptor and/or type II receptors (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a combination of antibodies thatcomprises a GDF8 antibody does not comprise a BMP9 antibody. In someembodiments, a combination of antibodies that comprises a GDF8 antibodydoes not comprise an activin A antibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least GDF11. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least GDF11. As used herein, a GDF11 antibody(or anti-GDF11 antibody) generally refers to an antibody that binds toGDF11 with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting GDF11. In certainembodiments, the extent of binding of a GDF11 antibody to an unrelated,non-GDF11 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%,2%, or less than about 1% of the binding of the antibody to GDF11 asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments, aGDF11 antibody binds to an epitope of GDF11 that is conserved amongGDF11 from different species. In certain preferred embodiments, ananti-GDF11 antibody binds to human GDF11. In some embodiments, a GDF11antibody may inhibit GDF11 from binding to a type I and/or type IIreceptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thusinhibit GDF11-mediated signaling (e.g., Smad signaling). In someembodiments, a GDF11 antibody may inhibit GDF11 from binding to aco-receptor and thus inhibit GDF11-mediated signaling (e.g., Smadsignaling). It should be noted that GDF11 has high sequence homology toGDF8 and therefore antibodies that bind to GDF11, in some instances, mayalso bind to and/or inhibit GDF8. In some embodiments, the disclosurerelates to a multispecific antibody (e.g., bi-specific antibody), anduses thereof, that binds to GDF11 and further binds to, for example, oneor more additional GDF/BMP ligands [e.g., activin (e.g., activin A,activin B, activin C, activin E, activin AB, activin AC, activin BC,activin AE, activin BE), GDF8, GDF3, BMP15, BMP10, and BMP6], one ormore type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB,ALK4, ALK5, and/or ALK7), and/or one or more co-receptors. In someembodiments, a multispecific antibody that binds to GDF11 does not bindor does not substantially bind to BMP9 (e.g., binds to BMP9 with a K_(D)of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a multispecificantibody that binds to GDF11 does not bind or does not substantiallybind to activin A (e.g., binds to activin A with a K_(D) of greater than1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about1×10⁻⁹ M). In some embodiments, the disclosure relates to combinationsof antibodies, and uses thereof, wherein the combination of antibodiescomprises a GDF11 antibody and one or more additional antibodies thatbind to, for example, one or more additional GDF/BMP ligands [e.g.,activin (e.g., activin A, activin B, activin C, activin E, activin AB,activin AC, activin BC, activin AE, activin BE), GDF8, GDF3, BMP6,BMP10, and BMP15], one or more type I receptor and/or type II receptors(e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a combination of antibodies thatcomprises a GDF11 antibody does not comprise a BMP9 antibody. In someembodiments, a combination of antibodies that comprises a GDF11 antibodydoes not comprise an activin A antibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least BMP6. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least BMP6. As used herein, a BMP6 antibody (oranti-BMP6 antibody) generally refers to an antibody that can bind toBMP6 with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting BMP6. In certainembodiments, the extent of binding of a BMP6 antibody to an unrelated,non-BMP6 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%,or less than about 1% of the binding of the antibody to BMP6 asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments, aBMP6 antibody binds to an epitope of BMP6 that is conserved among BMP6from different species. In certain preferred embodiments, an anti-BMP6antibody binds to human BMP6. In some embodiments, a BMP6 antibody mayinhibit BMP6 from binding to a type I and/or type II receptor (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibitBMP6-mediated signaling (e.g., Smad signaling). In some embodiments, aBMP6 antibody may inhibit BMP6 from binding to a co-receptor and thusinhibit BMP6-mediated signaling (e.g., Smad signaling). In someembodiments, the disclosure relates to a multispecific antibody (e.g.,bi-specific antibody), and uses thereof, that binds to BMP6 and furtherbinds to, for example, one or more additional GDF/BMP ligands [e.g.,activin (e.g., activin A, activin B, activin C, activin E, activin AB,activin AC, activin BC, activin AE, activin BE), GDF8, GDF3, BMP15,BMP10, and GDF11], one or more type I receptor and/or type II receptors(e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a multispecific antibody that bindsto BMP6 does not bind or does not substantially bind to BMP9 (e.g.,binds to BMP9 with a K_(D) of greater than 1×10⁻⁷ M or has relativelymodest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). In someembodiments, a multispecific antibody that binds to BMP6 does not bindor does not substantially bind to activin A (e.g., binds to activin Awith a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding,e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). In some embodiments, thedisclosure relates to combinations of antibodies, and uses thereof,wherein the combination of antibodies comprises a BMP6 antibody and oneor more additional antibodies that bind to, for example, one or moreadditional GDF/BMP ligands [e.g., activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin BC, activin AE,activin BE), GDF8, GDF11, GDF3, BMP10, and BMP15], one or more type Ireceptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5,and/or ALK7), and/or one or more co-receptors. In some embodiments, acombination of antibodies that comprises a BMP6 antibody does notcomprise a BMP9 antibody. In some embodiments, a combination ofantibodies that comprises a BMP6 antibody does not comprise an activin Aantibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least GDF3. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least GDF3. As used herein, a GDF3 antibody (oranti-GDF3antibody) generally refers to an antibody that can bind to GDF3with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting GDF3. In certainembodiments, the extent of binding of a GDF3 antibody to an unrelated,non-GDF3 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%,or less than about 1% of the binding of the antibody to GDF3 asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments, aGDF3 antibody binds to an epitope of GDF3 that is conserved among GDF3from different species. In certain preferred embodiments, an anti-GDF3antibody binds to human GDF3. In some embodiments, a GDF3 antibody mayinhibit GDF3 from binding to a type I and/or type II receptor (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibitGDF3-mediated signaling (e.g., Smad signaling). In some embodiments, aGDF3 antibody may inhibit GDF3 from binding to a co-receptor and thusinhibit GDF3-mediated signaling (e.g., Smad signaling). In someembodiments, the disclosure relates to a multispecific antibody (e.g.,bi-specific antibody), and uses thereof, that binds to GDF3 and furtherbinds to, for example, one or more additional GDF/BMP ligands [e.g.,activin (e.g., activin A, activin B, activin C, activin E, activin AB,activin AC, activin BC, activin AE, activin BE), GDF8, BMP6, BMP15,BMP10, and GDF11], one or more type I receptor and/or type II receptors(e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a multispecific antibody that bindsto GDF3 does not bind or does not substantially bind to BMP9 (e.g.,binds to BMP9 with a K_(D) of greater than 1×10⁻⁷M or has relativelymodest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). In someembodiments, a multispecific antibody that binds to GDF3 does not bindor does not substantially bind to activin A (e.g., binds to activin Awith a K_(D) of greater than 1×10⁻⁷M or has relatively modest binding,e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). In some embodiments, thedisclosure relates to combinations of antibodies, and uses thereof,wherein the combination of antibodies comprises a GDF3 antibody and oneor more additional antibodies that bind to, for example, one or moreadditional GDF/BMP ligands [e.g., activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin BC, activin AE,activin BE), GDF8, GDF11, BMP6, BMP10, and BMP15], one or more type Ireceptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5,and/or ALK7), and/or one or more co-receptors. In some embodiments, acombination of antibodies that comprises a GDF3 antibody does notcomprise a BMP9 antibody. In some embodiments, a combination ofantibodies that comprises a GDF3 antibody does not comprise an activin Aantibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least BMP15. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least BMP15. As used herein, a BMP15 antibody(or anti-BMP15 antibody) generally refers to an antibody that can bindto BMP15 with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting BMP15. In certainembodiments, the extent of binding of a BMP15 antibody to an unrelated,non-BMP15 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%,2%, or less than about 1% of the binding of the antibody to BMP15 asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments, aBMP15 antibody binds to an epitope of BMP15 that is conserved amongBMP15 from different species. In certain preferred embodiments, ananti-BMP15 antibody binds to human BMP15. In some embodiments, a BMP15antibody may inhibit BMP15 from binding to a type I and/or type IIreceptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thusinhibit BMP15-mediated signaling (e.g., Smad signaling). In someembodiments, a BMP15 antibody may inhibit BMP15 from binding to aco-receptor and thus inhibit BMP15-mediated signaling (e.g., Smadsignaling). In some embodiments, the disclosure relates to amultispecific antibody (e.g., bi-specific antibody), and uses thereof,that binds to BMP15 and further binds to, for example, one or moreadditional GDF/BMP ligands [e.g., activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin BC, activin AE andactivin BE), GDF8, GDF11, GDF3, BMP10, and BMP6], one or more type Ireceptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5,and/or ALK7), and/or one or more co-receptors. In some embodiments, amultispecific antibody that binds to BMP15 does not bind or does notsubstantially bind to BMP9 (e.g., binds to BMP9 with a K_(D) of greaterthan 1×10⁻⁷M or has relatively modest binding, e.g., about 1×10⁻⁸M orabout 1×10⁻⁹M). In some embodiments, a multispecific antibody that bindsto BMP15 does not bind or does not substantially bind to activin A(e.g., binds to activin A with a K_(D) of greater than 1×10⁻⁷ M or hasrelatively modest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). Insome embodiments, the disclosure relates to combinations of antibodies,and uses thereof, wherein the combination of antibodies comprises aBMP15 antibody and one or more additional antibodies that bind to, forexample, one or more additional GDF/BMP ligands [e.g., activin (e.g.,activin A, activin B, activin C, activin E, activin AB, activin AC,activin BC, activin AE and activin BE), GDF8, GDF3 BMP6, BMP10, andGDF11], one or more type I receptor and/or type II receptors (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a combination of antibodies thatcomprises a BMP15 antibody does not comprise a BMP9 antibody. In someembodiments, a combination of antibodies that comprises a BMP15 antibodydoes not comprise an activin A antibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least BMP10. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least BMP10. As used herein, a BMP10 antibody(or anti-BMP10 antibody) generally refers to an antibody that can bindto BMP10 with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting BMP10. In certainembodiments, the extent of binding of a BMP10 antibody to an unrelated,non-BMP10 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%,2%, or less than about 1% of the binding of the antibody to BMP10 asmeasured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein interaction or binding affinity assay. In certain embodiments, aBMP10 antibody binds to an epitope of BMP10 that is conserved amongBMP10 from different species. In certain preferred embodiments, ananti-BMP10 antibody binds to human BMP10. In some embodiments, a BMP10antibody may inhibit BMP10 from binding to a type I and/or type IIreceptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thusinhibit BMP10-mediated signaling (e.g., Smad signaling). In someembodiments, a BMP10 antibody may inhibit BMP10 from binding to aco-receptor and thus inhibit BMP10-mediated signaling (e.g., Smadsignaling). In some embodiments, the disclosure relates to amultispecific antibody (e.g., bi-specific antibody), and uses thereof,that binds to BMP10 and further binds to, for example, one or moreadditional GDF/BMP ligands [e.g., activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin BC, activin AE andactivin BE), GDF8, GDF11, GDF3, and BMP6], one or more type I receptorand/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/orALK7), and/or one or more co-receptors. In some embodiments, amultispecific antibody that binds to BMP10 does not bind or does notsubstantially bind to BMP9 (e.g., binds to BMP9 with a K_(D) of greaterthan 1×10⁻⁷M or has relatively modest binding, e.g., about 1×10⁻⁸M orabout 1×10⁻⁹M). In some embodiments, a multispecific antibody that bindsto BMP10 does not bind or does not substantially bind to activin A(e.g., binds to activin A with a K_(D) of greater than 1×10⁻⁷ M or hasrelatively modest binding, e.g., about 1×10⁻⁸M or about 1×10⁻⁹M). Insome embodiments, the disclosure relates to combinations of antibodies,and uses thereof, wherein the combination of antibodies comprises aBMP10 antibody and one or more additional antibodies that bind to, forexample, one or more additional GDF/BMP ligands [e.g., activin (e.g.,activin A, activin B, activin C, activin E, activin AB, activin AC,activin BC, activin AE and activin BE), GDF8, GDF3 BMP6, BMP10, andGDF11], one or more type I receptor and/or type II receptors (e.g.,ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or moreco-receptors. In some embodiments, a combination of antibodies thatcomprises a BMP10 antibody does not comprise a BMP9 antibody. In someembodiments, a combination of antibodies that comprises a BMP10 antibodydoes not comprise an activin A antibody.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least ActRIIB Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least ActRIIB As used herein, an ActRIIBantibody (anti-ActRIIB antibody) generally refers to an antibody thatbinds to ActRIIB with sufficient affinity such that the antibody isuseful as a diagnostic and/or therapeutic agent in targeting ActRIIB Incertain embodiments, the extent of binding of an anti-ActRIIB antibodyto an unrelated, non-ActRIIB protein is less than about 10%, 9%, 8%, 7%,6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibodyto ActRIIB as measured, for example, by a radioimmunoassay (RIA),Biacore, or other protein-protein interaction or binding affinity assay.In certain embodiments, an anti-ActRIIB antibody binds to an epitope ofActRIIB that is conserved among ActRIIB from different species. Incertain preferred embodiments, an anti-ActRIIB antibody binds to humanActRIIB In some embodiments, an anti-ActRIIB antibody may inhibit one ormore GDF/BMP ligands [e.g., GDF8, activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin BC, activin AE andactivin BE) GDF11, BMP6, GDF3, BMP10, and BMP15] from binding to ActRIIBIn some embodiments, an anti-ActRIIB antibody is a multispecificantibody (e.g., bi-specific antibody) that binds to ActRIIB and one ormore GDF/BMP ligands [e.g., GDF11, GDF8, activin (e.g., activin A,activin B, activin C, activin E, activin AB, activin AC) GDF3, BMP6, andBMP10], type I receptor (e.g., ALK4, ALK5, and/or ALK7), co-receptor,and/or an additional type II receptor (e.g., ActRIIA). In someembodiments, the disclosure relates to combinations of antibodies, anduses thereof, wherein the combination of antibodies comprises ananti-ActRIIB antibody and one or more additional antibodies that bindto, for example, one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and activin BE) BMP6, GDF3, and BMP10],co-receptors, type I receptors (e.g., ALK4, ALK5, and/or ALK7), and/oradditional type II receptors (e.g., ActRIIA). It should be noted thatActRIIB has sequence similarity to ActRIIA and therefore antibodies thatbind to ActRIIB, in some instances, may also bind to and/or inhibitActRIIA.

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least ActRIIA. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least ActRIIA. As used herein, an ActRIIAantibody (anti-ActRIIA antibody) generally refers to an antibody thatbinds to ActRIIA with sufficient affinity such that the antibody isuseful as a diagnostic and/or therapeutic agent in targeting ActRIIA. Incertain embodiments, the extent of binding of an anti-ActRIIA antibodyto an unrelated, non-ActRIIA protein is less than about 10%, 9%, 8%, 7%,6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibodyto ActRIIA as measured, for example, by a radioimmunoassay (RIA),Biacore, or other protein-protein interaction or binding affinity assay.In certain embodiments, an anti-ActRIIA antibody binds to an epitope ofActRIIA that is conserved among ActRIIA from different species. Incertain preferred embodiments, an anti-ActRIIA antibody binds to humanActRIIA. In some embodiments, an anti-ActRIIA antibody may inhibit oneor more GDF/BMP ligands [e.g., GDF8, activin (e.g., activin A, activinB, activin C, activin E, activin AB, activin AC, activin BC, activin AEand activin BE) GDF11, BMP6, GDF3, BMP10, and BMP15] from binding toActRIIA. In some embodiments, an anti-ActRIIA antibody is amultispecific antibody (e.g., bi-specific antibody) that binds toActRIIA and one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC) GDF3, BMP6, and BMP10], type I receptor (e.g., ALK4, ALK5, and/orALK7), co-receptor, and/or an additional type II receptor (e.g.,ActRIIB) In some embodiments, the disclosure relates to combinations ofantibodies, and uses thereof, wherein the combination of antibodiescomprises an anti-ActRIIA antibody and one or more additional antibodiesthat bind to, for example, one or more GDF/BMP ligands [e.g., GDF11,GDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and activin BE) BMP6, and BMP10],co-receptors, type I receptors (e.g., ALK4, ALK5, and/or ALK7), and/oradditional type II receptors (e.g., ActRIIB) It should be noted thatActRIIA has sequence similarity to ActRIIB and therefore antibodies thatbind to ActRIIA, in some instances, may also bind to and/or inhibitActRIIB

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least ALK4. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least ALK4. As used herein, an ALK4 antibody(anti-ALK4 antibody) generally refers to an antibody that binds to ALK4with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting ALK4. In certainembodiments, the extent of binding of an anti-ALK4 antibody to anunrelated, non-ALK4 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%,4%, 3%, 2%, or less than about 1% of the binding of the antibody to ALK4as measured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein-protein interaction or binding affinity assay. In certainembodiments, an anti-ALK4 antibody binds to an epitope of ALK4 that isconserved among ALK4 from different species. In certain preferredembodiments, an anti-ALK4 antibody binds to human ALK4. In someembodiments, an anti-ALK4 antibody may inhibit one or more GDF/BMPligands [e.g., GDF8, activin (e.g., activin A, activin B, activin C,activin E, activin AB, activin AC, activin BC, activin AE and activinBE) GDF11, BMP6, GDF3, BMP10, and BMP15] from binding to ALK4. In someembodiments, an anti-ALK4 antibody is a multispecific antibody (e.g.,bi-specific antibody) that binds to ALK4 and one or more GDF/BMP ligands[e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C,activin E, activin AB, activin AC) GDF3, BMP6, and BMP10], type IIreceptor (e.g., ActRIIA and/or ActRIIB), co-receptor, and/or anadditional type I receptor (e.g., ALK5 and/or ALK7). In someembodiments, the disclosure relates to combinations of antibodies, anduses thereof, wherein the combination of antibodies comprises ananti-ALK4 antibody and one or more additional antibodies that bind to,for example, one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and activin BE) BMP6, and BMP10],co-receptors, type II receptors (e.g., ActRIIA and/or ActRIIB), and/oradditional type I receptors (e.g., ALK5 and/or ALK7).

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least ALK5. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least ALK5. As used herein, an ALK5 antibody(anti-ALK5 antibody) generally refers to an antibody that binds to ALK5with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting ALK5. In certainembodiments, the extent of binding of an anti-ALK5 antibody to anunrelated, non-ALK5 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%,4%, 3%, 2%, or less than about 1% of the binding of the antibody to ALK5as measured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein-protein interaction or binding affinity assay. In certainembodiments, an anti-ALK5 antibody binds to an epitope of ALK5 that isconserved among ALK5 from different species. In certain preferredembodiments, an anti-ALK5 antibody binds to human ALK5. In someembodiments, an anti-ALK5 antibody may inhibit one or more GDF/BMPligands [e.g., GDF8, activin (e.g., activin A, activin B, activin C,activin E, activin AB, activin AC, activin BC, activin AE and activinBE) GDF11, BMP6, GDF3, BMP10, and BMP15] from binding to ALK5. In someembodiments, an anti-ALK5 antibody is a multispecific antibody (e.g.,bi-specific antibody) that binds to ALK5 and one or more GDF/BMP ligands[e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C,activin E, activin AB, activin AC) GDF3, BMP6, and BMP10], type IIreceptor (e.g., ActRIIA and/or ActRIIB), co-receptor, and/or anadditional type I receptor (e.g., ALK4 and/or ALK7). In someembodiments, the disclosure relates to combinations of antibodies, anduses thereof, wherein the combination of antibodies comprises ananti-ALK5 antibody and one or more additional antibodies that bind to,for example, one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and activin BE) BMP6, and BMP10],co-receptors, type II receptors (e.g., ActRIIA and/or ActRIIB), and/oradditional type I receptors (e.g., ALK4 and/or ALK7).

In certain aspects, a GDF/BMP antagonist antibody, or combination ofantibodies, is an antibody that inhibits at least ALK7. Therefore, insome embodiments, a GDF/BMP antagonist antibody, or combination ofantibodies, binds to at least ALK7. As used herein, an ALK7 antibody(anti-ALK7 antibody) generally refers to an antibody that binds to ALK7with sufficient affinity such that the antibody is useful as adiagnostic and/or therapeutic agent in targeting ALK7. In certainembodiments, the extent of binding of an anti-ALK7 antibody to anunrelated, non-ALK7 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%,4%, 3%, 2%, or less than about 1% of the binding of the antibody to ALK7as measured, for example, by a radioimmunoassay (RIA), Biacore, or otherprotein-protein interaction or binding affinity assay. In certainembodiments, an anti-ALK7 antibody binds to an epitope of ALK7 that isconserved among ALK7 from different species. In certain preferredembodiments, an anti-ALK7 antibody binds to human ALK7. In someembodiments, an anti-ALK7 antibody may inhibit one or more GDF/BMPligands [e.g., GDF8, activin (e.g., activin A, activin B, activin C,activin E, activin AB, activin AC, activin BC, activin AE and activinBE) GDF11, BMP6, GDF3, BMP10, and BMP15] from binding to ALK7. In someembodiments, an anti-ALK7 antibody is a multispecific antibody (e.g.,bi-specific antibody) that binds to ALK7 and one or more GDF/BMP ligands[e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C,activin E, activin AB, activin AC) GDF3, BMP6, and BMP10], type IIreceptor (e.g., ActRIIA and/or ActRIIB), co-receptor, and/or anadditional type I receptor (e.g., ALK4 and/or ALK5). In someembodiments, the disclosure relates to combinations of antibodies, anduses thereof, wherein the combination of antibodies comprises ananti-ALK7 antibody and one or more additional antibodies that bind to,for example, one or more GDF/BMP ligands [e.g., GDF11, GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and activin BE) BMP6, and BMP10],co-receptors, type II receptors (e.g., ActRIIA and/or ActRIIB), and/oradditional type I receptors (e.g., ALK4 and/or ALK5).

The term antibody is used herein in the broadest sense and encompassesvarious antibody structures, including but not limited to monoclonalantibodies, polyclonal antibodies, multispecific antibodies (e.g.,bispecific antibodies), and antibody fragments so long as they exhibitthe desired antigen-binding activity. An antibody fragment refers to amolecule other than an intact antibody that comprises a portion of anintact antibody that binds the antigen to which the intact antibodybinds. Examples of antibody fragments include, but are not limited to,Fv, Fab, Fab′, Fab′-SH, F(ab′)₂; diabodies; linear antibodies;single-chain antibody molecules (e.g., scFv); and multispecificantibodies formed from antibody fragments [see, e.g., Hudson et al.(2003) Nat. Med. 9:129-134; Plückthun, in The Pharmacology of MonoclonalAntibodies, vol. 113, Rosenburg and Moore eds., (Springer-Verlag, NewYork), pp. 269-315 (1994); WO 93/16185; and U.S. Pat. Nos. 5,571,894;5,587,458; and 5,869,046]. Diabodies are antibody fragments with twoantigen-binding sites that may be bivalent or bispecific [see, e.g., EP404,097; WO 1993/01161; Hudson et al. (2003) Nat. Med. 9:129-134 (2003);and Hollinger et al. (1993) Proc. Natl. Acad. Sci. USA 90: 6444-6448].Triabodies and tetrabodies are also described in Hudson et al. (2003)Nat. Med. 9:129-134. Single-domain antibodies are antibody fragmentscomprising all or a portion of the heavy-chain variable domain or all ora portion of the light-chain variable domain of an antibody. In certainembodiments, a single-domain antibody is a human single-domain antibody[see, e.g., U.S. Pat. No. 6,248,516]. Antibodies disclosed herein may bepolyclonal antibodies or monoclonal antibodies. In certain embodiments,the antibodies of the present disclosure comprise a label attachedthereto and able to be detected (e.g., the label can be a radioisotope,fluorescent compound, enzyme, or enzyme co-factor). In certain preferredembodiments, the antibodies of the present disclosure are isolatedantibodies. In certain preferred embodiments, the antibodies of thepresent disclosure are recombinant antibodies.

The antibodies herein may be of any class. The class of an antibodyrefers to the type of constant domain or constant region possessed byits heavy chain. There are five major classes of antibodies: IgA, IgD,IgE, IgG, and IgM, and several of these may be further divided intosubclasses (isotypes), for example, IgG₁, IgG₂, IgG₃, IgG₄, IgA₁, andIgA₂. The heavy chain constant domains that correspond to the differentclasses of immunoglobulins are called alpha, delta, epsilon, gamma, andmu.

In general, an antibody for use in the methods disclosed hereinspecifically binds to its target antigen, preferably with high bindingaffinity. Affinity may be expressed as a K_(D) value and reflects theintrinsic binding affinity (e.g., with minimized avidity effects).Typically, binding affinity is measured in vitro, whether in a cell-freeor cell-associated setting. Any of a number of assays known in the art,including those disclosed herein, can be used to obtain binding affinitymeasurements including, for example, Biacore, radiolabeledantigen-binding assay (RIA), and ELISA. In some embodiments, antibodiesof the present disclosure bind to their target antigens (e.g. ActRIIB,ActRIIA, ALK4, ALK5, ALK7, activin, GDF11, GDF8, GDF3, BMP15, BMP10,and/or BMP6) with at least a K_(D) of 1×10⁻⁷ or stronger, 1×10⁻⁸ orstronger, 1×10⁻⁹ or stronger, 1×10⁻¹⁰ or stronger, 1×10⁻¹¹ or stronger,1×10⁻¹² or stronger, 1×10¹³ or stronger, or 1×10⁻¹⁴ or stronger.

In certain embodiments, K_(D) is measured by RIA performed with the Fabversion of an antibody of interest and its target antigen as describedby the following assay. Solution binding affinity of Fabs for theantigen is measured by equilibrating Fab with a minimal concentration ofradiolabeled antigen (e.g., ¹²⁵I-labeled) in the presence of a titrationseries of unlabeled antigen, then capturing bound antigen with ananti-Fab antibody-coated plate [see, e.g., Chen et al. (1999) J. Mol.Biol. 293:865-881]. To establish conditions for the assay, multi-wellplates (e.g., MICROTITER® from Thermo Scientific) are coated (e.g.,overnight) with a capturing anti-Fab antibody (e.g., from Cappel Labs)and subsequently blocked with bovine serum albumin, preferably at roomtemperature (approximately 23° C.). In a non-adsorbent plate,radiolabeled antigen are mixed with serial dilutions of a Fab ofinterest [e.g., consistent with assessment of the anti-VEGF antibody,Fab-12, in Presta et al., (1997) Cancer Res. 57:4593-4599]. The Fab ofinterest is then incubated, preferably overnight but the incubation maycontinue for a longer period (e.g., about 65 hours) to ensure thatequilibrium is reached. Thereafter, the mixtures are transferred to thecapture plate for incubation, preferably at room temperature for aboutone hour. The solution is then removed and the plate is washed timesseveral times, preferably with polysorbate 20 and PBS mixture. When theplates have dried, scintillant (e.g., MICROSCINT® from Packard) isadded, and the plates are counted on a gamma counter (e.g., TOPCOUNT®from Packard).

According to another embodiment, K_(D) is measured using surface plasmonresonance assays using, for example a BIACORE® 2000 or a BIACORE® 3000(BIAcore, Inc., Piscataway, N.J.) with immobilized antigen CM5 chips atabout 10 response units (RU). Briefly, carboxymethylated dextranbiosensor chips (CM5, BIACORE, Inc.) are activated withN-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) andN-hydroxysuccinimide (NHS) according to the supplier's instructions. Forexample, an antigen can be diluted with 10 mM sodium acetate, pH 4.8, to5 μg/ml (about 0.2 μM) before injection at a flow rate of 5 μl/minute toachieve approximately 10 response units (RU) of coupled protein.Following the injection of antigen, 1 M ethanolamine is injected toblock unreacted groups. For kinetics measurements, two-fold serialdilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05%polysorbate 20 (TWEEN-20®) surfactant (PBST) at at a flow rate ofapproximately 25 μl/min. Association rates (k_(on)) and dissociationrates (k_(off)) are calculated using, for example, a simple one-to-oneLangmuir binding model (BIACORE® Evaluation Software version 3.2) bysimultaneously fitting the association and dissociation sensorgrams. Theequilibrium dissociation constant (K_(D)) is calculated as the ratiok_(off)/k_(on) [see, e.g., Chen et al., (1999) J. Mol. Biol.293:865-881]. If the on-rate exceeds, for example, 10⁶M⁻¹ s⁻¹ by thesurface plasmon resonance assay above, then the on-rate can bedetermined by using a fluorescent quenching technique that measures theincrease or decrease in fluorescence emission intensity (e.g.,excitation=295 nm; emission=340 nm, 16 nm band-pass) of a 20 nManti-antigen antibody (Fab form) in PBS in the presence of increasingconcentrations of antigen as measured in a spectrometer, such as astop-flow equipped spectrophometer (Aviv Instruments) or a 8000-seriesSLM-AMINCO® spectrophotometer (ThermoSpectronic) with a stirred cuvette.

Antibody fragments can be made by various techniques, including but notlimited to proteolytic digestion of an intact antibody as well asproduction by recombinant host cells (e.g., E. coli or phage), asdescribed herein. The nucleic acid and amino acid sequences of humanActRIIA, ActRIIB, ALK4, ALK5, ALK7, activin (activin A, activin B,activin C, and activin E), GDF11, GDF8, BMP15, GDF3, BMP10, and BMP6,are known in the art. In addition, numerous methods for generatingantibodies are well known in the art, some of which are describedherein. Therefore antibody antagonists for use in accordance with thisdisclosure may be routinely made by the skilled person in the art basedon the knowledge in the art and teachings provided herein.

In certain embodiments, an antibody provided herein is a chimericantibody. A chimeric antibody refers to an antibody in which a portionof the heavy and/or light chain is derived from a particular source orspecies, while the remainder of the heavy and/or light chain is derivedfrom a different source or species. Certain chimeric antibodies aredescribed, for example, in U.S. Pat. No. 4,816,567; and Morrison et al.,(1984) Proc. Natl. Acad. Sci. USA, 81:6851-6855. In some embodiments, achimeric antibody comprises a non-human variable region (e.g., avariable region derived from a mouse, rat, hamster, rabbit, or non-humanprimate, such as a monkey) and a human constant region. In someembodiments, a chimeric antibody is a “class switched” antibody in whichthe class or subclass has been changed from that of the parent antibody.In general, chimeric antibodies include antigen-binding fragmentsthereof.

In certain embodiments, a chimeric antibody provided herein is ahumanized antibody. A humanized antibody refers to a chimeric antibodycomprising amino acid residues from non-human hypervariable regions(HVRs) and amino acid residues from human framework regions (FRs). Incertain embodiments, a humanized antibody will comprise substantiallyall of at least one, and typically two, variable domains, in which allor substantially all of the HVRs (e.g., CDRs) correspond to those of anon-human antibody, and all or substantially all of the FRs correspondto those of a human antibody. A humanized antibody optionally maycomprise at least a portion of an antibody constant region derived froma human antibody. A “humanized form” of an antibody, e.g., a non-humanantibody, refers to an antibody that has undergone humanization.Humanized antibodies and methods of making them are reviewed, forexample, in Almagro and Fransson (2008) Front. Biosci. 13:1619-1633 andare further described, for example, in Riechmann et al., (1988) Nature332:323-329; Queen et al. (1989) Proc. Nat'l Acad. Sci. USA86:10029-10033; U.S. Pat. Nos. 5,821,337; 7,527,791; 6,982,321; and7,087,409; Kashmiri et al., (2005) Methods 36:25-34 [describing SDR(a-CDR) grafting]; Padlan, Mol. Immunol. (1991) 28:489-498 (describing“resurfacing”); Dall'Acqua et al. (2005) Methods 36:43-60 (describing“FR shuffling”); Osbourn et al. (2005) Methods 36:61-68; and Klimka etal. Br. J. Cancer (2000) 83:252-260 (describing the “guided selection”approach to FR shuffling). Human framework regions that may be used forhumanization include but are not limited to: framework regions selectedusing the “best-fit” method [see, e.g., Sims et al. (1993) J. Immunol.151:2296]; framework regions derived from the consensus sequence ofhuman antibodies of a particular subgroup of light or heavy chainvariable regions [see, e.g., Carter et al. (1992) Proc. Natl. Acad. Sci.USA, 89:4285; and Presta et al. (1993) J. Immunol., 151:2623]; humanmature (somatically mutated) framework regions or human germlineframework regions [see, e.g., Almagro and Fransson (2008) Front. Biosci.13:1619-1633]; and framework regions derived from screening FR libraries[see, e.g., Baca et al., (1997) J. Biol. Chem. 272:10678-10684; andRosok et al., (1996) J. Biol. Chem. 271:22611-22618].

In certain embodiments, an antibody provided herein is a human antibody.Human antibodies can be produced using various techniques known in theart. Human antibodies are described generally in van Dijk and van deWinkel (2008) Curr. Opin. Pharmacol. 5: 368-74 (2001) and Lonberg, Curr.Opin. Immunol. 20:450-459. For example, human antibodies may be preparedby administering an immunogen (e.g., a GDF11 polypeptide, an activin Bpolypeptide, an ActRIIA polypeptide, or an ActRIIB polypeptide) to atransgenic animal that has been modified to produce intact humanantibodies or intact antibodies with human variable regions in responseto antigenic challenge. Such animals typically contain all or a portionof the human immunoglobulin loci, which replace the endogenousimmunoglobulin loci, or which are present extrachromosomally orintegrated randomly into the animal's chromosomes. In such transgenicanimals, the endogenous immunoglobulin loci have generally beeninactivated. For a review of methods for obtaining human antibodies fromtransgenic animals see, for example, Lonberg (2005) Nat. Biotech.23:1117-1125; U.S. Pat. Nos. 6,075,181 and 6,150,584 (describingXENOMOUSE™ technology); U.S. Pat. No. 5,770,429 (describing HuMab®technology); U.S. Pat. No. 7,041,870 (describing K-M MOUSE® technology);and U.S. Patent Application Publication No. 2007/0061900 (describingVelociMouse® technology). Human variable regions from intact antibodiesgenerated by such animals may be further modified, for example, bycombining with a different human constant region.

Human antibodies provided herein can also be made by hybridoma-basedmethods. Human myeloma and mouse-human heteromyeloma cell lines for theproduction of human monoclonal antibodies have been described [see,e.g., Kozbor J. Immunol., (1984) 133: 3001; Brodeur et al. (1987)Monoclonal Antibody Production Techniques and Applications, pp. 51-63,Marcel Dekker, Inc., New York; and Boerner et al. (1991) J. Immunol.,147: 86]. Human antibodies generated via human B-cell hybridomatechnology are also described in Li et al., (2006) Proc. Natl. Acad.Sci. USA, 103:3557-3562. Additional methods include those described, forexample, in U.S. Pat. No. 7,189,826 (describing production of monoclonalhuman IgM antibodies from hybridoma cell lines) and Ni, XiandaiMianyixue (2006) 26(4):265-268 (2006) (describing human-humanhybridomas). Human hybridoma technology (Trioma technology) is alsodescribed in Vollmers and Brandlein (2005) Histol. Histopathol.,20(3):927-937 (2005) and Vollmers and Brandlein (2005) Methods Find Exp.Clin. Pharmacol., 27(3):185-91. Human antibodies provided herein mayalso be generated by isolating Fv clone variable-domain sequencesselected from human-derived phage display libraries. Suchvariable-domain sequences may then be combined with a desired humanconstant domain. Techniques for selecting human antibodies from antibodylibraries are known in the art and described herein.

For example, antibodies of the present disclosure may be isolated byscreening combinatorial libraries for antibodies with the desiredactivity or activities. A variety of methods are known in the art forgenerating phage display libraries and screening such libraries forantibodies possessing the desired binding characteristics. Such methodsare reviewed, for example, in Hoogenboom et al. (2001) in Methods inMolecular Biology 178:1-37, O'Brien et al., ed., Human Press, Totowa,N.J. and further described, for example, in the McCafferty et al. (1991)Nature 348:552-554; Clackson et al., (1991) Nature 352: 624-628; Markset al. (1992) J. Mol. Biol. 222:581-597; Marks and Bradbury (2003) inMethods in Molecular Biology 248:161-175, Lo, ed., Human Press, Totowa,N.J.; Sidhu et al. (2004) J. Mol. Biol. 338(2):299-310; Lee et al.(2004) J. Mol. Biol. 340(5):1073-1093; Fellouse (2004) Proc. Natl. Acad.Sci. USA 101(34):12467-12472; and Lee et al. (2004) J. Immunol. Methods284(1-2): 119-132.

In certain phage display methods, repertoires of VH and VL genes areseparately cloned by polymerase chain reaction (PCR) and recombinedrandomly in phage libraries, which can then be screened forantigen-binding phage as described in Winter et al. (1994) Ann. Rev.Immunol., 12: 433-455. Phage typically display antibody fragments,either as single-chain Fv (scFv) fragments or as Fab fragments.Libraries from immunized sources provide high-affinity antibodies to theimmunogen (e.g., ActRIIA, ActRIIB, activin, GDF11, GDF8, BMP15, GDF3, orBMP6) without the requirement of constructing hybridomas. Alternatively,the naive repertoire can be cloned (e.g., from human) to provide asingle source of antibodies to a wide range of non-self and alsoself-antigens without any immunization as described by Griffiths et al.(1993) EMBO J, 12: 725-734. Finally, naive libraries can also be madesynthetically by cloning unrearranged V-gene segments from stem cells,and using PCR primers containing random sequence to encode the highlyvariable CDR3 regions and to accomplish rearrangement in vitro, asdescribed by Hoogenboom and Winter (1992) J. Mol. Biol., 227: 381-388.Patent publications describing human antibody phage libraries include,for example: U.S. Pat. No. 5,750,373, and U.S. Patent Publication Nos.2005/0079574, 2005/0119455, 2005/0266000, 2007/0117126, 2007/0160598,2007/0237764, 2007/0292936, and 2009/0002360.

In certain embodiments, an antibody provided herein is a multispecificantibody, for example, a bispecific antibody. Multispecific antibodies(typically monoclonal antibodies) that have binding specificities for atleast two different epitopes (e.g., two, three, four, five, or six ormore) on one or more (e.g., two, three, four, five, six or more)antigens.

Techniques for making multispecific antibodies include, but are notlimited to, recombinant co-expression of two immunoglobulinheavy-chain/light-chain pairs having different specificities [see, e.g.,Milstein and Cuello (1983) Nature 305: 537; International patentpublication no. WO 93/08829; and Traunecker et al. (1991) EMBO J. 10:3655, and U.S. Pat. No. 5,731,168 (“knob-in-hole” engineering)].Multispecific antibodies may also be made by engineering electrostaticsteering effects for making antibody Fc-heterodimeric molecules (see,e.g., WO 2009/089004A1); cross-linking two or more antibodies orfragments [see, e.g., U.S. Pat. No. 4,676,980; and Brennan et al. (1985)Science, 229: 81]; using leucine zippers to produce bispecificantibodies [see, e.g., Kostelny et al. (1992) J. Immunol.,148(5):1547-1553]; using “diabody” technology for making bispecificantibody fragments [see, e.g., Hollinger et al. (1993) Proc. Natl. Acad.Sci. USA, 90:6444-6448]; using single-chain Fv (sFv) dimers [see, e.g.,Gruber et al. (1994) J. Immunol., 152:5368]; and preparing trispecificantibodies (see, e.g., Tutt et al. (1991) J. Immunol. 147: 60.Multispecific antibodies can be prepared as full-length antibodies orantibody fragments. Engineered antibodies with three or more functionalantigen-binding sites, including “Octopus antibodies,” are also includedherein [see, e.g., US 2006/0025576A1].

In certain embodiments, an antibody disclosed herein is a monoclonalantibody. Monoclonal antibody refers to an antibody obtained from apopulation of substantially homogeneous antibodies, i.e., the individualantibodies comprising the population are identical and/or bind the sameepitope, except for possible variant antibodies, e.g., containingnaturally occurring mutations or arising during production of amonoclonal antibody preparation, such variants generally being presentin minor amounts. In contrast to polyclonal antibody preparations, whichtypically include different antibodies directed against differentepitopes, each monoclonal antibody of a monoclonal antibody preparationis directed against a single epitope on an antigen. Thus, the modifier“monoclonal” indicates the character of the antibody as being obtainedfrom a substantially homogeneous population of antibodies, and is not tobe construed as requiring production of the antibody by any particularmethod. For example, the monoclonal antibodies to be used in accordancewith the present methods may be made by a variety of techniques,including but not limited to the hybridoma method, recombinant DNAmethods, phage-display methods, and methods utilizing transgenic animalscontaining all or part of the human immunoglobulin loci, such methodsand other exemplary methods for making monoclonal antibodies beingdescribed herein.

For example, by using immunogens derived from activin,anti-protein/anti-peptide antisera or monoclonal antibodies can be madeby standard protocols [see, e.g., Antibodies: A Laboratory Manual ed. byHarlow and Lane (1988) Cold Spring Harbor Press: 1988]. A mammal, suchas a mouse, hamster, or rabbit, can be immunized with an immunogenicform of the activin polypeptide, an antigenic fragment which is capableof eliciting an antibody response, or a fusion protein. Techniques forconferring immunogenicity on a protein or peptide include conjugation tocarriers or other techniques well known in the art. An immunogenicportion of a activin polypeptide can be administered in the presence ofadjuvant. The progress of immunization can be monitored by detection ofantibody titers in plasma or serum. Standard ELISA or other immunoassayscan be used with the immunogen as antigen to assess the levels ofantibody production and/or level of binding affinity.

Following immunization of an animal with an antigenic preparation ofactivin, antisera can be obtained and, if desired, polyclonal antibodiescan be isolated from the serum. To produce monoclonal antibodies,antibody-producing cells (lymphocytes) can be harvested from animmunized animal and fused by standard somatic cell fusion procedureswith immortalizing cells such as myeloma cells to yield hybridoma cells.Such techniques are well known in the art, and include, for example, thehybridoma technique [see, e.g., Kohler and Milstein (1975) Nature, 256:495-497], the human B cell hybridoma technique [see, e.g., Kozbar et al.(1983) Immunology Today, 4:72], and the EBV-hybridoma technique toproduce human monoclonal antibodies [Cole et al. (1985) MonoclonalAntibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96]. Hybridomacells can be screened immunochemically for production of antibodiesspecifically reactive with a activin polypeptide, and monoclonalantibodies isolated from a culture comprising such hybridoma cells.

In certain embodiments, one or more amino acid modifications may beintroduced into the Fc region of an antibody provided herein therebygenerating an Fc region variant. The Fc region variant may comprise ahuman Fc region sequence (e.g., a human IgG1, IgG2, IgG3 or IgG4 Fcregion) comprising an amino acid modification (e.g., a substitution,deletion, and/or addition) at one or more amino acid positions.

For example, the present disclosure contemplates an antibody variantthat possesses some but not all effector functions, which make it adesirable candidate for applications in which the half-life of theantibody in vivo is important yet certain effector functions [e.g.,complement-dependent cytotoxicity (CDC) and antibody-dependent cellularcytotoxicity (ADCC)] are unnecessary or deleterious. In vitro and/or invivo cytotoxicity assays can be conducted to confirm thereduction/depletion of CDC and/or ADCC activities. For example, Fcreceptor (FcR) binding assays can be conducted to ensure that theantibody lacks FcγR binding (hence likely lacking ADCC activity), butretains FcRn binding ability. The primary cells for mediating ADCC, NKcells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII andFcγRIII FcR expression on hematopoietic cells is summarized in, forexample, Ravetch and Kinet (1991) Annu. Rev. Immunol. 9:457-492.Non-limiting examples of in vitro assays to assess ADCC activity of amolecule of interest are described in U.S. Pat. No. 5,500,362;Hellstrom, I. et al. (1986) Proc. Natl. Acad. Sci. USA 83:7059-7063];Hellstrom, I et al. (1985) Proc. Natl. Acad. Sci. USA 82:1499-1502; U.S.Pat. No. 5,821,337; Bruggemann, M. et al. (1987) J. Exp. Med.166:1351-1361. Alternatively, non-radioactive assays methods may beemployed (e.g., ACTI™, non-radioactive cytotoxicity assay for flowcytometry; CellTechnology, Inc. Mountain View, Calif.; and CytoTox 96®non-radioactive cytotoxicity assay, Promega, Madison, Wis.). Usefuleffector cells for such assays include peripheral blood mononuclearcells (PBMC) and natural killer (NK) cells. Alternatively, oradditionally, ADCC activity of the molecule of interest may be assessedin vivo, for example, in an animal model such as that disclosed inClynes et al. (1998) Proc. Natl. Acad. Sci. USA 95:652-656. C1q bindingassays may also be carried out to confirm that the antibody is unable tobind C1q and hence lacks CDC activity [see, e.g., C1q and C3c bindingELISA in WO 2006/029879 and WO 2005/100402]. To assess complementactivation, a CDC assay may be performed [see, e.g, Gazzano-Santoro etal. (1996) J. Immunol. Methods 202:163; Cragg, M. S. et al. (2003) Blood101:1045-1052; and Cragg, M. S, and M. J. Glennie (2004) Blood103:2738-2743]. FcRn binding and in vivo clearance/half-lifedeterminations can also be performed using methods known in the art[see, e.g., Petkova, S. B. et al. (2006) Intl. Immunol.18(12):1759-1769]. Antibodies of the present disclosure with reducedeffector function include those with substitution of one or more of Fcregion residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Pat. No.6,737,056). Such Fc mutants include Fc mutants with substitutions at twoor more of amino acid positions 265, 269, 270, 297 and 327, includingthe so-called “DANA” Fc mutant with substitution of residues 265 and 297to alanine (U.S. Pat. No. 7,332,581).

In certain embodiments, it may be desirable to create cysteineengineered antibodies, e.g., “thioMAbs,” in which one or more residuesof an antibody are substituted with cysteine residues. In particularembodiments, the substituted residues occur at accessible sites of theantibody. By substituting those residues with cysteine, reactive thiolgroups are thereby positioned at accessible sites of the antibody andmay be used to conjugate the antibody to other moieties, such as drugmoieties or linker-drug moieties, to create an immunoconjugate, asdescribed further herein. In certain embodiments, any one or more of thefollowing residues may be substituted with cysteine: V205 (Kabatnumbering) of the light chain; A118 (EU numbering) of the heavy chain;and S400 (EU numbering) of the heavy chain Fc region. Cysteineengineered antibodies may be generated as described, for example, inU.S. Pat. No. 7,521,541.

In addition, the techniques used to screen antibodies in order toidentify a desirable antibody may influence the properties of theantibody obtained. For example, if an antibody is to be used for bindingan antigen in solution, it may be desirable to test solution binding. Avariety of different techniques are available for testing interactionsbetween antibodies and antigens to identify particularly desirableantibodies. Such techniques include ELISAs, surface plasmon resonancebinding assays (e.g., the Biacore binding assay, Biacore AB, Uppsala,Sweden), sandwich assays (e.g., the paramagnetic bead system of IGENInternational, Inc., Gaithersburg, Md.), western blots,immunoprecipitation assays, and immunohistochemistry.

In certain embodiments, amino acid sequence variants of the antibodiesand/or the binding polypeptides provided herein are contemplated. Forexample, it may be desirable to improve the binding affinity and/orother biological properties of the antibody and/or binding polypeptide.Amino acid sequence variants of an antibody and/or binding polypeptidesmay be prepared by introducing appropriate modifications into thenucleotide sequence encoding the antibody and/or binding polypeptide, orby peptide synthesis. Such modifications include, for example, deletionsfrom, and/or insertions into and/or substitutions of residues within theamino acid sequences of the antibody and/or binding polypeptide. Anycombination of deletion, insertion, and substitution can be made toarrive at the final construct, provided that the final constructpossesses the desired characteristics, e.g., target-binding (e.g., andactivin such as activin E and/or activin C binding).

Alterations (e.g., substitutions) may be made in HVRs, for example, toimprove antibody affinity. Such alterations may be made in HVR“hotspots,” i.e., residues encoded by codons that undergo mutation athigh frequency during the somatic maturation process [see, e.g.,Chowdhury (2008) Methods Mol. Biol. 207:179-196 (2008)], and/or SDRs(a-CDRs), with the resulting variant VH or VL being tested for bindingaffinity. Affinity maturation by constructing and reselecting fromsecondary libraries has been described in the art [see, e.g., Hoogenboomet al., in Methods in Molecular Biology 178:1-37, O'Brien et al., ed.,Human Press, Totowa, N.J., (2001). In some embodiments of affinitymaturation, diversity is introduced into the variable genes chosen formaturation by any of a variety of methods (e.g., error-prone PCR, chainshuffling, or oligonucleotide-directed mutagenesis). A secondary libraryis then created. The library is then screened to identify any antibodyvariants with the desired affinity. Another method to introducediversity involves HVR-directed approaches, in which several HVRresidues (e.g., 4-6 residues at a time) are randomized. HVR residuesinvolved in antigen binding may be specifically identified, e.g., usingalanine scanning mutagenesis or modeling. CDR-H3 and CDR-L3 inparticular are often targeted.

In certain embodiments, substitutions, insertions, or deletions mayoccur within one or more HVRs so long as such alterations do notsubstantially reduce the ability of the antibody to bind to the antigen.For example, conservative alterations (e.g., conservative substitutionsas provided herein) that do not substantially reduce binding affinitymay be made in HVRs. Such alterations may be outside of HVR “hotspots”or SDRs. In certain embodiments of the variant VH and VL sequencesprovided above, each HVR either is unaltered, or contains no more thanone, two or three amino acid substitutions.

A useful method for identification of residues or regions of theantibody and/or the binding polypeptide that may be targeted formutagenesis is called “alanine scanning mutagenesis” as described byCunningham and Wells (1989) Science, 244:1081-1085. In this method, aresidue or group of target residues (e.g., charged residues such as Arg,Asp, His, Lys, and Glu) are identified and replaced by a neutral ornegatively charged amino acid (e.g., alanine or polyalanine) todetermine whether the interaction of the antibody-antigen is affected.Further substitutions may be introduced at the amino acid locationsdemonstrating functional sensitivity to the initial substitutions.Alternatively, or additionally, a crystal structure of anantigen-antibody complex is determined to identify contact pointsbetween the antibody and antigen. Such contact residues and neighboringresidues may be targeted or eliminated as candidates for substitution.Variants may be screened to determine whether they contain the desiredproperties.

Amino acid sequence insertions include amino- and/or carboxyl-terminalfusions ranging in length from one residue to polypeptides containing ahundred or more residues, as well as intrasequence insertions of singleor multiple amino acid residues. Examples of terminal insertions includean antibody with an N-terminal methionyl residue. Other insertionalvariants of the antibody molecule include the fusion of the N- orC-terminus of the antibody to an enzyme (e.g., for ADEPT) or apolypeptide which increases the serum half-life of the antibody.

In certain embodiments, an antibody and/or binding polypeptide providedherein may be further modified to contain additional nonproteinaceousmoieties that are known in the art and readily available. The moietiessuitable for derivatization of the antibody and/or binding polypeptideinclude but are not limited to water soluble polymers. Non-limitingexamples of water soluble polymers include, but are not limited to,polyethylene glycol (PEG), copolymers of ethylene glycol/propyleneglycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, ethylene/maleicanhydride copolymer, polyaminoacids (either homopolymers or randomcopolymers), and dextran or poly(n-vinyl pyrrolidone)polyethyleneglycol, propropylene glycol homopolymers, prolypropylene oxide/ethyleneoxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinylalcohol, and mixtures thereof. Polyethylene glycol propionaldehyde mayhave advantages in manufacturing due to its stability in water. Thepolymer may be of any molecular weight, and may be branched orunbranched. The number of polymers attached to the antibody and/orbinding polypeptide may vary, and if more than one polymer are attached,they can be the same or different molecules. In general, the numberand/or type of polymers used for derivatization can be determined basedon considerations including, but not limited to, the particularproperties or functions of the antibody and/or binding polypeptide to beimproved, whether the antibody derivative and/or binding polypeptidederivative will be used in a therapy under defined conditions.

5. Small Molecule Antagonists

In other aspects, a GDF/BMP antagonist to be used in accordance with themethods and uses described herein is a small molecule (GDF/BMP smallmolecule antagonist), or combination of small molecule antagonists. AGDF/BMP small molecule antagonist, or combination of small moleculeantagonists, may inhibit, for example, one or more GDF/BMP ligands(e.g., activin, GDF11, GDF8, GDF3, BMP6, BMP10, and/or BMP15), a type Ireceptor (e.g., ALK4, ALK5, and/or ALK7), a type II receptor (e.g.,ActRIIB and/or ActRIIA), a co-receptor, and/or one or more signalingfactors (e.g. Smad proteins such as Smads 2 and 3). In some embodiments,a GDF/BMP small molecule antagonist, or combination of small moleculeantagonists, inhibits signaling mediated by one or more GDF/BMP ligands,for example, as determined in a cell-based assay such as those describedherein. As described herein, GDF/BMP small molecule antagonists may beused, alone or in combination with one or more supportive therapies oractive agents, to treat, prevent, or reduce the progression rate and/orseverity of pulmonary hypertension (PH), particularly treating,preventing or reducing the progression rate and/or severity of one ormore PH-associated complications.

In some embodiments, a GDF/BMP small molecule antagonist, or combinationof small molecule antagonists, inhibits at least GDF11, optionallyfurther inhibiting one or more of GDF8, activin (e.g., activin A,activin B, activin C, activin E, activin AB, activin AC, activin BC,activin AE and/or activin BE), GDF3, BMP6, BMP10, ActRIIA, ActRIIB,ALK4, ALK5, ALK7, and one or more Smad proteins (e.g., Smads 2 and 3).In some embodiments, a GDF/BMP small molecule antagonist, or combinationof small molecule antagonists, inhibits at least GDF8, optionallyfurther inhibiting one or more of GDF11, activin (e.g., activin A,activin B, activin C, activin E, activin AB, activin AC, activin BC,activin AE and/or activin BE), GDF3, BMP6, BMP10, ActRIIA, ActRIIB,ALK4, ALK5, ALK7, and one or more Smad proteins (e.g., Smads 2 and 3).In some embodiments, a GDF/BMP small molecule antagonist, or combinationof small molecule antagonists, inhibits at least activin (activin A,activin B, activin C, activin E, activin AB, activin AC, activin BC,activin AE and/or activin BE), optionally further inhibiting one or moreof GDF8, GDF11, GDF3, BMP6, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7,and one or more Smad proteins (e.g., Smads 2 and 3). In someembodiments, a GDF/BMP small molecule antagonist, or combination ofsmall molecule antagonists, inhibits at least activin B, optionallyfurther inhibiting one or more of GDF8, GDF11, GDF3, BMP6, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g.,Smads 2 and 3). In some embodiments, a GDF/BMP small moleculeantagonist, or combination of small molecule antagonists, inhibits atleast BMP6, optionally further inhibiting one or more of GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and/or activin BE), GDF3, GDF11, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g.,Smads 2 and 3). In some embodiments, a GDF/BMP small moleculeantagonist, or combination of small molecule antagonists, inhibits atleast BMP15, optionally further inhibiting one or more of GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and/or activin BE), GDF3, BMP6, GDF11, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g.,Smads 2 and 3). In some embodiments, a GDF/BMP small moleculeantagonist, or combination of small molecule antagonists, inhibits atleast GDF3, optionally further inhibiting one or more of GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and/or activin BE), BMP15, BMP6, GDF11,BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins(e.g., Smads 2 and 3). In some embodiments, a GDF/BMP small moleculeantagonist, or combination of small molecule antagonists, inhibits atleast BMP10, optionally further inhibiting one or more of GDF8, activin(e.g., activin A, activin B, activin C, activin E, activin AB, activinAC, activin BC, activin AE and/or activin BE), BMP15, BMP6, GDF11, GDF3,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g.,Smads 2 and 3). In some embodiments, a GDF/BMP small moleculeantagonist, or combination of small molecule antagonists, inhibits atleast ActRIIA, optionally further inhibiting one or more of GDF8,activin (e.g., activin A, activin B, activin C, activin E, activin AB,activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, BMP10, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMP smallmolecule antagonist, or combination of small molecule antagonists,inhibits at least ActRIIB, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, BMP10, ALK4, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMP smallmolecule antagonist, or combination of small molecule antagonists,inhibits at least ALK4, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, BMP10, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMP smallmolecule antagonist, or combination of small molecule antagonists,inhibits at least ALK5, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, ALK4, BMP10, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMP smallmolecule antagonist, or combination of small molecule antagonists,inhibits at least ALK7, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, ALK4, ALK5, BMP10, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMP smallmolecule antagonist, or combination of small molecule antagonists, asdisclosed herein does not inhibit or does not substantially inhibitBMP9. In some embodiments, a GDF/BMP small molecule antagonist, orcombination of small molecule antagonists, as disclosed herein does notinhibit or does not substantially inhibit activin A.

GDF/BMP small molecule antagonists can be direct or indirect inhibitors.For example, an indirect small molecule antagonist, or combination ofsmall molecule antagonists, may inhibit the expression (e.g.,transcription, translation, cellular secretion, or combinations thereof)of at least one or more GDF/BMP ligands [e.g., activin (e.g., activin A,activin B, activin C, activin E, activin AB, activin AC, activin B,activin BC, activin AE, or activin BE), GDF11, BMP15, BMP6, GDF3, BMP10,and/or GDF8], type I receptor (e.g., ALK4, ALK5, and/or ALK7), type IIreceptors (e.g., ActRIIA and/or ActRIIB), co-receptor, and/or one ormore downstream signaling components (e.g., Smads). Alternatively, adirect small molecule antagonist, or combination of small moleculeantagonists, may directly bind to and inhibit, for example, one or moreone or more GDF/BMP ligands [e.g., activin (e.g., activin A, activin B,activin C, activin E, activin AB, activin AC, activin B, activin BC,activin AE, or activin BE), GDF11, BMP15, BMP6, GDF3, BMP10, and/orGDF8], type I receptor (e.g., ALK4, ALK5 and/or ALK7), type II receptors(e.g., ActRIIA and/or ActRIIB), co-receptor, and/or one or moredownstream signaling components (e.g., Smads). Combinations of one ormore indirect and one or more direct GDF/BMP small molecule antagonistsmay be used in accordance with the methods disclosed herein.

Binding small-molecule antagonists of the present disclosure may beidentified and chemically synthesized using known methodology (see,e.g., PCT Publication Nos. WO 00/00823 and WO 00/39585). In general,small molecule antagonists of the disclosure are usually less than about2000 daltons in size, alternatively less than about 1500, 750, 500, 250or 200 daltons in size, wherein such organic small molecules that arecapable of binding, preferably specifically, to a polypeptide asdescribed herein. These small molecule antagonists may be identifiedwithout undue experimentation using well-known techniques. In thisregard, it is noted that techniques for screening organic small-moleculelibraries for molecules that are capable of binding to a polypeptidetarget are well known in the art (see, e.g., international patentpublication Nos. WO00/00823 and WO00/39585).

Binding organic small molecules of the present disclosure may be, forexample, aldehydes, ketones, oximes, hydrazones, semicarbazones,carbazides, primary amines, secondary amines, tertiary amines,N-substituted hydrazines, hydrazides, alcohols, ethers, thiols,thioethers, disulfides, carboxylic acids, esters, amides, ureas,carbamates, carbonates, ketals, thioketals, acetals, thioacetals, arylhalides, aryl sulfonates, alkyl halides, alkyl sulfonates, aromaticcompounds, heterocyclic compounds, anilines, alkenes, alkynes, diols,amino alcohols, oxazolidines, oxazolines, thiazolidines, thiazolines,enamines, sulfonamides, epoxides, aziridines, isocyanates, sulfonylchlorides, diazo compounds, and acid chlorides.

6. Polynucleotide Antagonists

In other aspects, a GDF/BMP antagonist to be used in accordance with themethods and uses disclosed herein is a polynucleotide (GDF/BMPpolynucleotide antagonist), or combination of polynucleotides. A GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,may inhibit, for example, one or more GDF/BMP ligands (e.g., activin,GDF11, GDF8, GDF3, BMP6, BMP10, and/or BMP15), type I receptors (e.g.,ALK4, ALK5, and/or ALK7), type II receptors (e.g., ActRIIA and/orActRIIB), co-receptor, and/or downstream signaling component (e.g.,Smads). In some embodiments, a GDF/BMP polynucleotide antagonist, orcombination of polynucleotide antagonists, inhibits signaling mediatedby one or more GDF/BMP ligands, for example, as determined in acell-based assay such as those described herein. As described herein,GDF/BMP polynucleotide antagonists may be used, alone or in combinationwith one or more supportive therapies or active agents, to treat,prevent, or reduce the progression rate and/or severity of pulmonaryhypertension (PH), particularly treating, preventing or reducing theprogression rate and/or severity of one or more PH-associatedcomplications

In some embodiments, a GDF/BMP polynucleotide antagonist, or combinationof polynucleotide antagonists, inhibits at least GDF11, optionallyfurther inhibiting one or more of GDF8, activin (e.g., activin A,activin B, activin C, activin E, activin AB, activin AC, activin BC,activin AE and/or activin BE), GDF3, BMP6, BMP15, BMP10, ActRIIA,ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g., Smads 2and 3). In some embodiments, a GDF/BMP polynucleotide antagonist, orcombination of polynucleotide antagonists, inhibits at least GDF8,optionally further inhibiting one or more of GDF11, activin (e.g.,activin A, activin B, activin C, activin E, activin AB, activin AC,activin BC, activin AE and/or activin BE), GDF3, BMP6, BMP15, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g.,Smads 2 and 3). In some embodiments, a GDF/BMP polynucleotideantagonist, or combination of polynucleotide antagonists, inhibits atleast activin (activin A, activin B, activin C, activin E, activin AB,activin AC, activin BC, activin AE and/or activin BE), optionallyfurther inhibiting one or more of GDF8, GDF11, GDF3, BMP6, BMP15, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins (e.g.,Smads 2 and 3). In some embodiments, a GDF/BMP polynucleotideantagonist, or combination of polynucleotide antagonists, inhibits atleast activin B, optionally further inhibiting one or more of GDF8,GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, andone or more Smad proteins (e.g., Smads 2 and 3). In some embodiments, aGDF/BMP polynucleotide antagonist, or combination of polynucleotideantagonists, inhibits at least BMP6, optionally further inhibiting oneor more of GDF8, activin (e.g., activin A, activin B, activin C, activinE, activin AB, activin AC, activin BC, activin AE and/or activin BE),GDF3, GDF11, BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and oneor more Smad proteins (e.g., Smads 2 and 3). In some embodiments, aGDF/BMP polynucleotide antagonist, or combination of polynucleotideantagonists, inhibits at least BMP15, optionally further inhibiting oneor more of GDF8, activin (e.g., activin A, activin B, activin C, activinE, activin AB, activin AC, activin BC, activin AE and/or activin BE),GDF3, BMP6, GDF11, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one ormore Smad proteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least GDF3, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least BMP10, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least ActRIIA, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, BMP10, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least ActRIIB, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, BMP10, ALK4, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least ALK4, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, BMP10, ALK5, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least ALK5, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, ALK4, BMP10, ALK7, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,inhibits at least ALK7, optionally further inhibiting one or more ofGDF8, activin (e.g., activin A, activin B, activin C, activin E, activinAB, activin AC, activin BC, activin AE and/or activin BE), BMP15, BMP6,GDF11, GDF3, ActRIIA, ActRIIB, ALK4, ALK5, BMP10, and one or more Smadproteins (e.g., Smads 2 and 3). In some embodiments, a GDF/BMPpolynucleotide antagonist, or combination of polynucleotide antagonists,as disclosed herein does not inhibit or does not substantially inhibitBMP9. In some embodiments, a GDF/BMP polynucleotide antagonist, orcombination of polynucleotide antagonists, as disclosed herein does notinhibit or does not substantially inhibit activin A.

In some embodiments, the polynucleotide antagonists of the disclosuremay be an antisense nucleic acid, an RNAi molecule [e.g., smallinterfering RNA (siRNA), small-hairpin RNA (shRNA), microRNA (miRNA)],an aptamer and/or a ribozyme. The nucleic acid and amino acid sequencesof human GDF11, GDF8, activin (activin A, activin B, activin C, andactivin E), BMP6, GDF3, ActRIIA, ActRIIB, BMP10, ALK4, ALK5, ALK7,BMP15, and Smad proteins are known in the art. In addition, manydifferent methods of generating polynucleotide antagonists are wellknown in the art. Therefore polynucleotide antagonists for use inaccordance with this disclosure may be routinely made by the skilledperson in the art based on the knowledge in the art and teachingsprovided herein.

Antisense technology can be used to control gene expression throughantisense DNA or RNA, or through triple-helix formation. Antisensetechniques are discussed, for example, in Okano (1991) J. Neurochem.56:560; Oligodeoxynucleotides as Antisense Inhibitors of GeneExpression, CRC Press, Boca Raton, Fla. (1988). Triple-helix formationis discussed in, for instance, Cooney et al. (1988) Science 241:456; andDervan et al., (1991) Science 251:1300. The methods are based on bindingof a polynucleotide to a complementary DNA or RNA. In some embodiments,the antisense nucleic acids comprise a single-stranded RNA or DNAsequence that is complementary to at least a portion of an RNAtranscript of a gene disclosed herein. However, absolutecomplementarity, although preferred, is not required.

A sequence “complementary to at least a portion of an RNA,” referred toherein, means a sequence having sufficient complementarity to be able tohybridize with the RNA, forming a stable duplex; in the case ofdouble-stranded antisense nucleic acids of a gene disclosed herein, asingle strand of the duplex DNA may thus be tested, or triplex formationmay be assayed. The ability to hybridize will depend on both the degreeof complementarity and the length of the antisense nucleic acid.Generally, the larger the hybridizing nucleic acid, the more basemismatches with an RNA it may contain and still form a stable duplex (ortriplex as the case may be). One skilled in the art can ascertain atolerable degree of mismatch by use of standard procedures to determinethe melting point of the hybridized complex.

Polynucleotides that are complementary to the 5′ end of the message, forexample, the 5′-untranslated sequence up to and including the AUGinitiation codon, should work most efficiently at inhibitingtranslation. However, sequences complementary to the 3′-untranslatedsequences of mRNAs have been shown to be effective at inhibitingtranslation of mRNAs as well [see, e.g., Wagner, R., (1994) Nature372:333-335]. Thus, oligonucleotides complementary to either the 5′- or3′-non-translated, non-coding regions of a gene of the disclosure, couldbe used in an antisense approach to inhibit translation of an endogenousmRNA. Polynucleotides complementary to the 5′-untranslated region of themRNA should include the complement of the AUG start codon. Antisensepolynucleotides complementary to mRNA coding regions are less efficientinhibitors of translation but could be used in accordance with themethods of the present disclosure. Whether designed to hybridize to the5′-, 3′- or coding region of an mRNA of the disclosure, antisensenucleic acids should be at least six nucleotides in length, and arepreferably oligonucleotides ranging from 6 to about 50 nucleotides inlength. In specific aspects the oligonucleotide is at least 10nucleotides, at least 17 nucleotides, at least 25 nucleotides or atleast 50 nucleotides.

In one embodiment, the antisense nucleic acid of the present disclosureis produced intracellularly by transcription from an exogenous sequence.For example, a vector or a portion thereof is transcribed, producing anantisense nucleic acid (RNA) of a gene of the disclosure.

Such a vector would contain a sequence encoding the desired antisensenucleic acid. Such a vector can remain episomal or become chromosomallyintegrated, as long as it can be transcribed to produce the desiredantisense RNA. Such vectors can be constructed by recombinant DNAtechnology methods standard in the art. Vectors can be plasmid, viral,or others known in the art, used for replication and expression invertebrate cells. Expression of the sequence encoding desired genes ofthe instant disclosure, or fragments thereof, can be by any promoterknown in the art to act in vertebrate, preferably human cells. Suchpromoters can be inducible or constitutive. Such promoters include, butare not limited to, the SV40 early promoter region [see, e.g., Benoistand Chambon (1981) Nature 290:304-310], the promoter contained in the 3′long-terminal repeat of Rous sarcoma virus [see, e.g., Yamamoto et al.(1980) Cell 22:787-797], the herpes thymidine promoter [see, e.g.,Wagner et al. (1981) Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445], andthe regulatory sequences of the metallothionein gene [see, e.g.,Brinster, et al. (1982) Nature 296:39-42].

In some embodiments, the polynucleotide antagonists are interfering RNA(RNAi) molecules that target the expression of one or more of: GDF11,GDF8, activin (activin A, activin B, activin C, and activin E), BMP6,GDF3, ActRIIA, ActRIIB, BMP10, ALK4, ALK5, ALK7, BMP15, and Smadproteins. RNAi refers to the expression of an RNA which interferes withthe expression of the targeted mRNA. Specifically, RNAi silences atargeted gene via interacting with the specific mRNA through a siRNA(small interfering RNA). The ds RNA complex is then targeted fordegradation by the cell. An siRNA molecule is a double-stranded RNAduplex of 10 to 50 nucleotides in length, which interferes with theexpression of a target gene which is sufficiently complementary (e.g. atleast 80% identity to the gene). In some embodiments, the siRNA moleculecomprises a nucleotide sequence that is at least 85, 90, 95, 96, 97, 98,99, or 100% identical to the nucleotide sequence of the target gene.

Additional RNAi molecules include short-hairpin RNA (shRNA); alsoshort-interfering hairpin and microRNA (miRNA). The shRNA moleculecontains sense and antisense sequences from a target gene connected by aloop. The shRNA is transported from the nucleus into the cytoplasm, andit is degraded along with the mRNA. Pol III or U6 promoters can be usedto express RNAs for RNAi. Paddison et al. [Genes & Dev. (2002)16:948-958, 2002] have used small RNA molecules folded into hairpins asa means to affect RNAi. Accordingly, such short-hairpin RNA (shRNA)molecules are also advantageously used in the methods described herein.The length of the stem and loop of functional shRNAs varies; stemlengths can range anywhere from about 25 to about 30 nt, and loop sizecan range between 4 to about 25 nt without affecting silencing activity.While not wishing to be bound by any particular theory, it is believedthat these shRNAs resemble the double-stranded RNA (dsRNA) products ofthe DICER RNase and, in any event, have the same capacity for inhibitingexpression of a specific gene. The shRNA can be expressed from alentiviral vector. An miRNA is a single-stranded RNA of about 10 to 70nucleotides in length that are initially transcribed as pre-miRNAcharacterized by a “stem-loop” structure, which are subsequentlyprocessed into mature miRNA after further processing through the RISC.

Molecules that mediate RNAi, including without limitation siRNA, can beproduced in vitro by chemical synthesis (Hohjoh, FEBS Lett 521:195-199,2002), hydrolysis of dsRNA (Yang et al., Proc Natl Acad Sci USA99:9942-9947, 2002), by in vitro transcription with T7 RNA polymerase(Donzeet et al., Nucleic Acids Res 30:e46, 2002; Yu et al., Proc NatlAcad Sci USA 99:6047-6052, 2002), and by hydrolysis of double-strandedRNA using a nuclease such as E. coli RNase III (Yang et al., Proc NatlAcad Sci USA 99:9942-9947, 2002).

According to another aspect, the disclosure provides polynucleotideantagonists including but not limited to, a decoy DNA, a double-strandedDNA, a single-stranded DNA, a complexed DNA, an encapsulated DNA, aviral DNA, a plasmid DNA, a naked RNA, an encapsulated RNA, a viral RNA,a double-stranded RNA, a molecule capable of generating RNAinterference, or combinations thereof.

In some embodiments, the polynucleotide antagonists of the disclosureare aptamers. Aptamers are nucleic acid molecules, includingdouble-stranded DNA and single-stranded RNA molecules, which bind to andform tertiary structures that specifically bind to a target molecule.The generation and therapeutic use of aptamers are well established inthe art (see, e.g., U.S. Pat. No. 5,475,096). Additional information onaptamers can be found in U.S. Patent Application Publication No.20060148748. Nucleic acid aptamers are selected using methods known inthe art, for example via the Systematic Evolution of Ligands byExponential Enrichment (SELEX) process. SELEX is a method for the invitro evolution of nucleic acid molecules with highly specific bindingto target molecules as described in, e.g., U.S. Pat. Nos. 5,475,096;5,580,737; 5,567,588; 5,707,796; 5,763,177; 6,011,577; and 6,699,843.Another screening method to identify aptamers is described in U.S. Pat.No. 5,270,163. The SELEX process is based on the capacity of nucleicacids for forming a variety of two- and three-dimensional structures, aswell as the chemical versatility available within the nucleotidemonomers to act as ligands (form specific binding pairs) with virtuallyany chemical compound, whether monomeric or polymeric, including othernucleic acid molecules and polypeptides. Molecules of any size orcomposition can serve as targets. The SELEX method involves selectionfrom a mixture of candidate oligonucleotides and step-wise iterations ofbinding, partitioning and amplification, using the same generalselection scheme, to achieve desired binding affinity and selectivity.Starting from a mixture of nucleic acids, which can comprise a segmentof randomized sequence, the SELEX method includes steps of contactingthe mixture with the target under conditions favorable for binding;partitioning unbound nucleic acids from those nucleic acids which havebound specifically to target molecules; dissociating the nucleicacid-target complexes; amplifying the nucleic acids dissociated from thenucleic acid-target complexes to yield a ligand enriched mixture ofnucleic acids. The steps of binding, partitioning, dissociating andamplifying are repeated through as many cycles as desired to yieldnucleic acid ligands which bind with high affinity and specificity tothe target molecule.

Typically, such binding molecules are separately administered to theanimal [see, e.g., O'Connor (1991) J. Neurochem. 56:560], but suchbinding molecules can also be expressed in vivo from polynucleotidestaken up by a host cell and expressed in vivo [see, e.g.,Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRCPress, Boca Raton, Fla. (1988)].

7. Follistatin and FLRG Antagonists

In other aspects, a GDF/BMP antagonist is a follistatin or FLRGpolypeptide. As described herein, follistatin and/or FLRG polypeptidesmay be used treat, prevent, or reduce the progression rate and/orseverity of pulmonary hypertension (PH), particularly treating,preventing or reducing the progression rate and/or severity of one ormore PH-associated complications.

The term “follistatin polypeptide” includes polypeptides comprising anynaturally occurring polypeptide of follistatin as well as any variantsthereof (including mutants, fragments, fusions, and peptidomimeticforms) that retain a useful activity, and further includes anyfunctional monomer or multimer of follistatin. In certain preferredembodiments, follistatin polypeptides of the disclosure bind to and/orinhibit activin activity, particularly activin A. Variants offollistatin polypeptides that retain activin binding properties can beidentified based on previous studies involving follistatin and activininteractions. For example, WO2008/030367 discloses specific follistatindomains (“FSDs”) that are shown to be important for activin binding. Asshown below in SEQ ID NOs: 28-30, the follistatin N-terminal domain(“FSND” SEQ ID NO: 28), FSD2 (SEQ ID NO: 30), and to a lesser extentFSD1 (SEQ ID NO: 29) represent exemplary domains within follistatin thatare important for activin binding. In addition, methods for making andtesting libraries of polypeptides are described above in the context ofActRII polypeptides, and such methods also pertain to making and testingvariants of follistatin. Follistatin polypeptides include polypeptidesderived from the sequence of any known follistatin having a sequence atleast about 80% identical to the sequence of a follistatin polypeptide,and optionally at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or greateridentity. Examples of follistatin polypeptides include the maturefollistatin polypeptide or shorter isoforms or other variants of thehuman follistatin precursor polypeptide (SEQ ID NO: 26) as described,for example, in WO2005/025601.

The human follistatin precursor polypeptide isoform FST344 is asfollows:

1 MVRARHQPGG LCLLLLLLCQ FMEDRSAQAG NCWLRQAKNG RCQVLYKTEL 51SKEECCSTGR LSTSWTEEDV NDNTLFKWMI FNGGAPNCIP CKETCENVDC 101GPGKKCRMNK KNKPRCVCAP DCSNITWKGP VCGLDGKTYR NECALLKARC 151KEQPELEVQY QGRCKKTCRD VFCPGSSTCV VDQTNNAYCV TCNRICPEPA 201SSEQYLCGND GVTYSSACHL RKATCLLGRS IGLAYEGKCI KAKSCEDIQC 251TGGKKCLWDF KVGRGRCSLC DELCPDSKSD EPVCASDNAT YASECAMKEA 301ACSSGVLLEV KHSGSCNSIS EDTEEEEEDE DQDYSFPISS ILEW(SEQ ID NO: 26; NCBI Reference No. NP_037541.1)

The signal peptide is underlined; also underlined above are the last 27residues which represent the C-terminal extension distinguishing thisfollistatin isoform from the shorter follistatin isoform FST317 shownbelow.

The human follistatin precursor polypeptide isoform FST317 is asfollows:

1 MVRARHQPGG LCLLLLLLCQ FMEDRSAQAG NCWLRQAKNG RCQVLYKTEL 51SKEECCSTGR LSTSWTEEDV NDNTLFKWMI FNGGAPNCIP CKETCENVDC 101GPGKKCRMNK KNKPRCVCAP DCSNITWKGP VCGLDGKTYR NECALLKARC 151KEQPELEVQY QGRCKKTCRD VFCPGSSTCV VDQTNNAYCV TCNRICPEPA 201SSEQYLCGND GVTYSSACHL RKATCLLGRS IGLAYEGKCI KAKSCEDIQC 251TGGKKCLWDF KVGRGRCSLC DELCPDSKSD EPVCASDNAT YASECAMKEA 301ACSSGVLLEV KHSGSCN (SEQ ID NO: 27; NCBI Reference No. NP_006341.1)The signal peptide is underlined.

The follistatin N-terminal domain (FSND) sequence is as follows:

(SEQ ID NO: 28; FSND)GNCWLRQAKNGRCQVLYKTELSKEECCSTGRLSTSWTEEDVNDNTLFKWMI FNGGAPNCIPCK

The FSD1 and FSD2 sequences are as follows:

(SEQ ID NO: 29; FSD1) ETCENVDCGPGKKCRMNKKNKPRCV (SEQ ID NO: 30; FSD2)KTCRDVFCPGSSTCVVDQTNNAYCVT

In other aspects, an agent for use in accordance with the methodsdisclosed herein is a follistatin-like related gene (FLRG), also knownas follistatin-related protein 3 (FSTL3). The term “FLRG polypeptide”includes polypeptides comprising any naturally occurring polypeptide ofFLRG as well as any variants thereof (including mutants, fragments,fusions, and peptidomimetic forms) that retain a useful activity. Incertain preferred embodiments, FLRG polypeptides of the disclosure bindto and/or inhibit activin activity, particularly activin A. Variants ofFLRG polypeptides that retain activin binding properties can beidentified using routine methods to assay FLRG and activin interactions(see, e.g., U.S. Pat. No. 6,537,966). In addition, methods for makingand testing libraries of polypeptides are described above in the contextof ActRII polypeptides and such methods also pertain to making andtesting variants of FLRG. FLRG polypeptides include polypeptides derivedfrom the sequence of any known FLRG having a sequence at least about 80%identical to the sequence of an FLRG polypeptide, and optionally atleast 85%, 90%, 95%, 97%, 99% or greater identity.

The human FLRG precursor (follistatin-related protein 3 precursor)polypeptide is as follows:

1 MRPGAPGPLW PLPWGALAWA VGFVSSMGSG NPAPGGVCWL QQGQEATCSL 51VLQTDVTRAE CCASGNIDTA WSNLTHPGNK INLLGFLGLV HCLPCKDSCD 101GVECGPGKAC RMLGGRPRCE CAPDCSGLPA RLQVCGSDGA TYRDECELRA 151ARCRGHPDLS VMYRGRCRKS CEHVVCPRPQ SCVVDQTGSA HCVVCRAAPC 201PVPSSPGQEL CGNNNVTYIS SCHMRQATCF LGRSIGVRHA GSCAGTPEEP 251PGGESAEEEE NFV (SEQ ID NO: 31; NCBI Reference No. NP_005851.1)The signal peptide is underlined.

In certain embodiments, functional variants or modified forms of thefollistatin polypeptides and FLRG polypeptides include fusion proteinshaving at least a portion of the follistatin polypeptide or FLRGpolypeptide and one or more fusion domains, such as, for example,domains that facilitate isolation, detection, stabilization ormultimerization of the polypeptide. Suitable fusion domains arediscussed in detail above with reference to the ActRII polypeptides. Insome embodiment, an antagonist agent of the disclosure is a fusionprotein comprising an activin-binding portion of a follistatinpolypeptide fused to an Fc domain. In another embodiment, an antagonistagent of the disclosure is a fusion protein comprising an activinbinding portion of an FLRG polypeptide fused to an Fc domain.

8. Screening Assays

In certain aspects, the present disclosure relates to the use of thesubject GDF/BMP antagonists (e.g., ActRII polypeptides and variantsthereof) to identify compounds (agents) which may be used to treat,prevent, or reduce the progression rate and/or severity of pulmonaryhypertension (PH), particularly treating, preventing or reducing theprogression rate and/or severity of one or more PH-associatedcomplications.

There are numerous approaches to screening for therapeutic agents fortreating PH by targeting signaling (e.g., Smad signaling) of one or moreGDF/BMP ligands. In certain embodiments, high-throughput screening ofcompounds can be carried out to identify agents that perturb GDF/BMPligands-mediated effects on a selected cell line. In certainembodiments, the assay is carried out to screen and identify compoundsthat specifically inhibit or reduce binding of an GDF/BMP ligand (e.g.,activin A, activin B, activin AB, activin C, GDF3, BMP6, GDF8, GDF15,GDF11 or BMP10) to its binding partner, such as an a type II receptor(e.g., ActRIIA and/or ActRIIB) Alternatively, the assay can be used toidentify compounds that enhance binding of a GDF/BMP ligand to itsbinding partner such as a type II receptor. In a further embodiment, thecompounds can be identified by their ability to interact with a type IIreceptor.

A variety of assay formats will suffice and, in light of the presentdisclosure, those not expressly described herein will nevertheless becomprehended by one of ordinary skill in the art. As described herein,the test compounds (agents) of the invention may be created by anycombinatorial chemical method. Alternatively, the subject compounds maybe naturally occurring biomolecules synthesized in vivo or in vitro.Compounds (agents) to be tested for their ability to act as modulatorsof tissue growth can be produced, for example, by bacteria, yeast,plants or other organisms (e.g., natural products), produced chemically(e.g., small molecules, including peptidomimetics), or producedrecombinantly. Test compounds contemplated by the present inventioninclude non-peptidyl organic molecules, peptides, polypeptides,peptidomimetics, sugars, hormones, and nucleic acid molecules. Incertain embodiments, the test agent is a small organic molecule having amolecular weight of less than about 2,000 Daltons.

The test compounds of the disclosure can be provided as single, discreteentities, or provided in libraries of greater complexity, such as madeby combinatorial chemistry. These libraries can comprise, for example,alcohols, alkyl halides, amines, amides, esters, aldehydes, ethers andother classes of organic compounds. Presentation of test compounds tothe test system can be in either an isolated form or as mixtures ofcompounds, especially in initial screening steps. Optionally, thecompounds may be optionally derivatized with other compounds and havederivatizing groups that facilitate isolation of the compounds.Non-limiting examples of derivatizing groups include biotin,fluorescein, digoxygenin, green fluorescent protein, isotopes,polyhistidine, magnetic beads, glutathione S-transferase (GST),photoactivatible crosslinkers or any combinations thereof.

In many drug-screening programs which test libraries of compounds andnatural extracts, high-throughput assays are desirable in order tomaximize the number of compounds surveyed in a given period of time.Assays which are performed in cell-free systems, such as may be derivedwith purified or semi-purified proteins, are often preferred as“primary” screens in that they can be generated to permit rapiddevelopment and relatively easy detection of an alteration in amolecular target which is mediated by a test compound. Moreover, theeffects of cellular toxicity or bioavailability of the test compound canbe generally ignored in the in vitro system, the assay instead beingfocused primarily on the effect of the drug on the molecular target asmay be manifest in an alteration of binding affinity between a GDF/BMPligand (e.g., activin A, activin B, activin AB, activin C, GDF8, GDF15,GDF11, GDF3, BMP6, or BMP10) to its binding partner, such as an a typeII receptor (e.g., ActRIIA and/or ActRIIB).

Merely to illustrate, in an exemplary screening assay of the presentdisclosure, the compound of interest is contacted with an isolated andpurified ActRIIB polypeptide which is ordinarily capable of binding toan ActRIIB ligand, as appropriate for the intention of the assay. To themixture of the compound and ActRIIB polypeptide is then added to acomposition containing an ActRIIB ligand (e.g., GDF11). Detection andquantification of ActRIIB/ActRIIB-ligand complexes provides a means fordetermining the compound's efficacy at inhibiting (or potentiating)complex formation between the ActRIIB polypeptide and its bindingprotein. The efficacy of the compound can be assessed by generatingdose-response curves from data obtained using various concentrations ofthe test compound. Moreover, a control assay can also be performed toprovide a baseline for comparison. For example, in a control assay,isolated and purified ActRIIB ligand is added to a compositioncontaining the ActRIIB polypeptide, and the formation of ActRIIB/ActRIIBligand complex is quantitated in the absence of the test compound. Itwill be understood that, in general, the order in which the reactantsmay be admixed can be varied, and can be admixed simultaneously.Moreover, in place of purified proteins, cellular extracts and lysatesmay be used to render a suitable cell-free assay system.

Complex formation between GDF/BMP ligand and its binding protein may bedetected by a variety of techniques. For instance, modulation of theformation of complexes can be quantitated using, for example, detectablylabeled proteins such as radiolabeled (e.g., ³²P ³⁵S, ¹⁴C or ³H),fluorescently labeled (e.g., FITC), or enzymatically labeled ActRIIBpolypeptide and/or its binding protein, by immunoassay, or bychromatographic detection.

In certain embodiments, the present disclosure contemplates the use offluorescence polarization assays and fluorescence resonance energytransfer (FRET) assays in measuring, either directly or indirectly, thedegree of interaction between a GDF/BMP ligand and its binding protein.Further, other modes of detection, such as those based on opticalwaveguides (see, e.g., PCT Publication WO 96/26432 and U.S. Pat. No.5,677,196), surface plasmon resonance (SPR), surface charge sensors, andsurface force sensors, are compatible with many embodiments of thedisclosure.

Moreover, the present disclosure contemplates the use of an interactiontrap assay, also known as the “two-hybrid assay,” for identifying agentsthat disrupt or potentiate interaction between a GDF/BMP ligand and itsbinding partner. See, e.g., U.S. Pat. No. 5,283,317; Zervos et al.(1993) Cell 72:223-232; Madura et al. (1993) J Biol Chem268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; andIwabuchi et al. (1993) Oncogene 8:1693-1696). In a specific embodiment,the present disclosure contemplates the use of reverse two-hybridsystems to identify compounds (e.g., small molecules or peptides) thatdissociate interactions between a GDF/BMP ligand and its binding protein[see, e.g., Vidal and Legrain, (1999) Nucleic Acids Res 27:919-29; Vidaland Legrain, (1999) Trends Biotechnol 17:374-81; and U.S. Pat. Nos.5,525,490; 5,955,280; and 5,965,368].

In certain embodiments, the subject compounds are identified by theirability to interact with a GDF/BMP ligand. The interaction between thecompound and the GDF/BMP ligand may be covalent or non-covalent. Forexample, such interaction can be identified at the protein level usingin vitro biochemical methods, including photo-crosslinking, radiolabeledligand binding, and affinity chromatography [see, e.g., Jakoby W B etal. (1974) Methods in Enzymology 46:1]. In certain cases, the compoundsmay be screened in a mechanism-based assay, such as an assay to detectcompounds which bind to a GDF/BMP ligand. This may include a solid-phaseor fluid-phase binding event. Alternatively, the gene encoding GDF/BMPligand can be transfected with a reporter system (e.g., β-galactosidase,luciferase, or green fluorescent protein) into a cell and screenedagainst the library preferably by high-throughput screening or withindividual members of the library. Other mechanism-based binding assaysmay be used; for example, binding assays which detect changes in freeenergy. Binding assays can be performed with the target fixed to a well,bead or chip or captured by an immobilized antibody or resolved bycapillary electrophoresis. The bound compounds may be detected usuallyusing colorimetric endpoints or fluorescence or surface plasmonresonance.

9. Therapeutic Uses

In part, the present disclosure relates to methods of treating pulmonaryhypertension (e.g., pulmonary arterial hypertension) comprisingadministering to a patient in need thereof an effective amount of aGDF/BMP antagonist (e.g., an antagonist of one or more of activin, GDF8,GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, andone or more Smad proteins). In some embodiments, the disclosurecontemplates methods of treating one or more complications of pulmonaryhypertension (e.g., smooth muscle and/or endothelial cell proliferationin the pulmonary artery, angiogenesis in the pulmonary artery, dyspnea,chest pain, pulmonary vascular remodeling, right ventricularhypertrophy, and pulmonary fibrosis) comprising administering to apatient in need thereof an effective amount of a GDF/BMP antagonist. Insome embodiments, the disclosure contemplates methods of preventing oneor more complications of pulmonary hypertension comprising administeringto a patient in need thereof an effective amount of a GDF/BMPantagonist. In some embodiments, the disclosure contemplates methods ofreducing the progression rate of pulmonary hypertension comprisingadministering to a patient in need thereof an effective amount of aGDF/BMP antagonist. In some embodiments, the disclosure contemplatesmethods of reducing the progression rate of one or more complications ofpulmonary hypertension comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist. In someembodiments, the disclosure contemplates methods of reducing theseverity of pulmonary hypertension comprising administering to a patientin need thereof an effective amount of a GDF/BMP antagonist. In someembodiments, the disclosure contemplates methods of reducing theseverity of one or more complications of pulmonary hypertensioncomprising administering to a patient in need thereof an effectiveamount of a GDF/BMP antagonist. Optionally, methods disclosed herein fortreating, preventing, or reducing the progression rate and/or severityof pulmonary hypertension, particularly treating, preventing, orreducing the progression rate and/or severity of one or morecomplications of pulmonary hypertension, may further compriseadministering to the patient one or more supportive therapies oradditional active agents for treating pulmonary hypertension. Forexample, the patient also may be administered one or more supportivetherapies or active agents selected from the group consisting of:prostacyclin and derivatives thereof (e.g., epoprostenol, treprostinil,and iloprost); prostacyclin receptor agonists (e.g., selexipag);endothelin receptor antagonists (e.g., thelin, ambrisentan, macitentan,and bosentan); calcium channel blockers (e.g., amlodipine, diltiazem,and nifedipine; anticoagulants (e.g., warfarin); diuretics; oxygentherapy; atrial septostomy; pulmonary thromboendarterectomy;phosphodiesterase type 5 inhibitors (e.g., sildenafil and tadalafil);activators of soluble guanylate cyclase (e.g., cinaciguat andriociguat); ASK-1 inhibitors (e.g., CIIA; SCH79797; GS-4997;MSC2032964A; 3H-naphtho[1,2,3-de]quiniline-2,7-diones, NQDI-1;2-thioxo-thiazolidines,5-bromo-3-(4-oxo-2-thioxo-thiazolidine-5-ylidene)-1,3-dihydro-indol-2-one);NF-κB antagonists (e.g., dh404, CDDO-epoxide; 2.2-difluoropropionamide;C28 imidazole (CDDO-Im); 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid(CDDO); 3-Acetyloleanolic Acid; 3-Triflouroacetyloleanolic Acid;28-Methyl-3-acetyloleanane; 28-Methyl-3-trifluoroacetyloleanane;28-Methyloxyoleanolic Acid; SZC014; SCZ015; SZC017; PEGylatedderivatives of oleanolic acid; 3-O-(beta-D-glucopyranosyl) oleanolicacid; 3-O-[beta-D-glucopyranosyl-(1- ->3)-beta-D-glucopyranosyl]oleanolic acid; 3-O-[beta-D-glucopyranosyl-(1-->2)-beta-D-glucopyranosyl] oleanolic acid;3-O-[beta-D-glucopyranosyl-(1- ->3)-beta-D-glucopyranosyl] oleanolicacid 28-O-beta-D-glucopyranosyl ester; 3-O-[beta-D-glucopyranosyl-(1-->2)-beta-D-glucopyranosyl] oleanolic acid 28-O-beta-D-glucopyranosylester; 3-O-[a-L-rhamnopyranosyl-(1- ->3)-beta-D-glucuronopyranosyl]oleanolic acid; 3-O-[alpha-L-rhamnopyranosyl-(1-->3)-beta-D-glucuronopyranosyl] oleanolic acid28-O-beta-D-glucopyranosyl ester; 28-O-β-D-glucopyranosyl-oleanolicacid; 3-O-β-D-glucopyranosyl (1→3)-3-D-glucopyranosiduronic acid (CS1);oleanolic acid 3-O-β-D-glucopyranosyl (1→3)-β-D-glucopyranosiduronicacid (CS2); methyl 3,11-dioxoolean-12-en-28-olate (DIOXOL); ZCVI₄-2;Benzyl 3-dehydr-oxy-1,2,5-oxadiazolo[3′,4′:2,3]oleanolate) lung and/orheart transplantation. In some embodiment, the patient may also beadministered a BMP9 polypeptide. In some embodiments the BMP9polypeptide is a mature BMP9 polypeptide. In some embodiments, the BMP9polypeptide comprises a BMP9 prodomain polypeptide. In some embodiments,the BMP9 polypeptide is administered in a pharmaceutical preparation,which optionally may comprise a BMP9 prodomain polypeptide. In such BMP9pharmaceutical preparations comprising a BMP9 prodomain polypeptide, theBMP9 polypeptide may be noncovalently associated with the BMP9 prodomainpolypeptide. In some embodiments, BMP9 pharmaceutical preparations aresubstantially free, or does not comprise, of BMP9 prodomain polypeptide.BMP9 polypeptides (mature and pro-polypeptides), BMP9 prodomainpolypeptides, pharmaceutical compositions comprising the same as well asmethod of generative such polypeptides and pharmaceutical compositionsare described in, for example, WO 2013/152213, which is incorporated byreference herein in its entirety. As used herein, a therapeutic that“prevents” a disorder or condition refers to a compound that, in astatistical sample, reduces the occurrence of the disorder or conditionin the treated sample relative to an untreated control sample, or delaysthe onset or reduces the severity of one or more symptoms of thedisorder or condition relative to the untreated control sample.

In some embodiments, the present disclosure relates to methods oftreating an interstitial lung disease (e.g., idiopathic pulmonaryfibrosis) comprising administering to a patient in need thereof aneffective amount of any of the GDF/BMP antagonists disclosed herein(e.g., an antagonist of one or more of activin, GDF8, GDF11, GDF3, BMP6,BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins). In some embodiments, the interstitial lung disease ispulmonary fibrosis. In some embodiments, the interstitial lung diseaseis caused by any one of the following: silicosis, asbestosis,berylliosis, hypersensitivity pneumonitis, drug use (e.g., antibiotics,chemotherapeutic drugs, antiarrhythmic agents, statins), systemicsclerosis, polymyositis, dermatomyositis, systemic lupus erythematosus,rheumatoid arthritis, an infection (e.g., atypical pneumonia,pneumocystis pneumonia, tuberculosis, chlamydia trachomatis, and/orrespiratory syncytial virus), lymphangitic carcinomatosis, cigarettesmoking, or developmental disorders. In some embodiments, theinterstitial lung disease is idiopathic (e.g., sarcoidosis, idiopathicpulmonary fibrosis, Hamman-Rich syndrome, and/or antisynthetasesyndrome). In particular embodiments, the interstitial lung disease isidiopathic pulmonary fibrosis. In some embodiments, the treatment foridiopathic pulmonary fibrosis is administered in combination with anadditional therapeutic agent. In some embodiments, the additionaltherapeutic agent is selected from the group consisting of: pirfenidone,N-acetylcysteine, prednisone, azathioprine, nintedanib, derivativesthereof and combinations thereof.

The term “treating” as used herein includes amelioration or eliminationof the condition once it has been established. In either case,prevention or treatment may be discerned in the diagnosis provided by aphysician or other health care provider and the intended result ofadministration of the therapeutic agent.

In general, treatment or prevention of a disease or condition asdescribed in the present disclosure is achieved by administering aGDF/BMP antagonist in an effective amount. An effective amount of anagent refers to an amount effective, at dosages and for periods of timenecessary, to achieve the desired therapeutic or prophylactic result. Atherapeutically effective amount of an agent of the present disclosuremay vary according to factors such as the disease state, age, sex, andweight of the individual, and the ability of the agent to elicit adesired response in the individual. A prophylactically effective amountrefers to an amount effective, at dosages and for periods of timenecessary, to achieve the desired prophylactic result.

The terms “subject,” an “individual,” or a “patient” are interchangeablethroughout the specification and generally refer to mammals. Mammalsinclude, but are not limited to, domesticated animals (e.g., cows,sheep, cats, dogs, and horses), primates (e.g., humans and non-humanprimates such as monkeys), rabbits, and rodents (e.g., mice and rats).

Pulmonary hypertension (PH) has been previously classified as primary(idiopathic) or secondary. Recently, the World Health Organization (WHO)has classified pulmonary hypertension into five groups: Group 1:pulmonary arterial hypertension (PAH); Group 2: pulmonary hypertensionwith left heart disease; Group 3: pulmonary hypertension with lungdisease and/or hypoxemia; Group 4: pulmonary hypertension due to chronicthrombotic and/or embolic disease; and Group 5: miscellaneous conditions(e.g., sarcoidosis, histiocytosis X, lymphangiomatosis and compressionof pulmonary vessels). See, for example, Rubin (2004) Chest 126:7-10.

In certain aspects, the disclosure relates to methods of treating,preventing, or reducing the progression rate and/or severity ofpulmonary hypertension (e.g., treating, preventing, or reducing theprogression rate and/or severity of one or more complications ofpulmonary hypertension) comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist (e.g., an antagonistof one or more of activin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins). Insome embodiments, the method relates to pulmonary hypertension patientsthat have pulmonary arterial hypertension. In some embodiments, themethod relates pulmonary hypertension patients that have pulmonaryhypertension with left heart disease. In some embodiments, the methodrelates to pulmonary hypertension patients that have lung disease and/orhypoxemia. In some embodiments, the method relates to pulmonaryhypertension patients that have chronic thrombotic and/or embolicdisease. In some embodiments, the method relates to pulmonaryhypertension patients that have sarcoidosis, histiocytosis X, orlymphangiomatosis and compression of pulmonary vessels.

Pulmonary arterial hypertension is a serious, progressive andlife-threatening disease of the pulmonary vasculature, characterized byprofound vasoconstriction and an abnormal proliferation of smooth musclecells in the walls of the pulmonary arteries. Severe constriction of theblood vessels in the lungs leads to very high pulmonary arterialpressures. These high pressures make it difficult for the heart to pumpblood through the lungs to be oxygenated. Patients with PAH suffer fromextreme shortness of breath as the heart struggles to pump against thesehigh pressures. Patients with PAH typically develop significantincreases in pulmonary vascular resistance (PVR) and sustainedelevations in pulmonary artery pressure (PAP), which ultimately lead toright ventricular failure and death. Patients diagnosed with PAH have apoor prognosis and equally compromised quality of life, with a mean lifeexpectancy of 2 to 5 years from the time of diagnosis if untreated.

A variety of factors contribute to the pathogenesis of pulmonaryhypertension including proliferation of pulmonary cells which cancontribute to vascular remodeling (i.e., hyperplasia). For example,pulmonary vascular remodeling occurs primarily by proliferation ofarterial endothelial cells and smooth muscle cells of patients withpulmonary hypertension. Overexpression of various cytokines is believedto promote pulmonary hypertension. Further, it has been found thatpulmonary hypertension may rise from the hyperproliferation of pulmonaryarterial smooth cells and pulmonary endothelial cells. Still further,advanced PAH may be characterized by muscularization of distal pulmonaryarterioles, concentric intimal thickening, and obstruction of thevascular lumen by proliferating endothelial cells. Pietra et al., J. Am.Coll. Cardiol., 43:255-325 (2004).

In certain aspects, the disclosure relates to methods of treating,preventing, or reducing the progression rate and/or severity ofpulmonary hypertension (e.g., treating, preventing, or reducing theprogression rate and/or severity of one or more complications ofpulmonary hypertension) comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist (e.g., an antagonistof one or more of activin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins),wherein the patient has resting pulmonary arterial pressure (PAP) of atleast 25 mm Hg (e.g., 25, 30, 35, 40, 45, or 50 mm Hg). In someembodiments, the method relates to patients having a resting PAP of atleast 25 mm Hg. In some embodiments, the method relates to patientshaving a resting PAP of at least 30 mm Hg. In some embodiments, themethod relates to patients having a resting PAP of at least 35 mm Hg. Insome embodiments, the method relates to patients having a resting PAP ofat least 40 mm Hg. In some embodiments, the method relates to patientshaving a resting PAP of at least 45 mm Hg. In some embodiments, themethod relates to patients having a resting PAP of at least 50 mm Hg.

In some embodiments, the disclosure relates to methods of adjusting oneor more hemodynamic parameters in the PH patient toward a more normallevel (e.g., normal as compared to healthy people of similar age andsex), comprising administering to a patient in need thereof an effectiveamount of a GDF/BMP antagonist (e.g., an antagonist of one or more ofactivin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB, ALK4,ALK5, ALK7, and one or more Smad proteins). In some embodiments, themethod relates to reducing PAP. In some embodiments, the method relatesto reducing the patient's PAP by at least 3 mmHg. In certainembodiments, the method relates to reducing the patient's PAP by atleast 5 mmHg. In certain embodiments, the method relates to reducing thepatient's PAP by at least 7 mmHg. In certain embodiments, the methodrelates to reducing the patient's PAP by at least 10 mmHg. In certainembodiments, the method relates to reducing the patient's PAP by atleast 12 mmHg. In certain embodiments, the method relates to reducingthe patient's PAP by at least 15 mmHg. In certain embodiments, themethod relates to reducing the patient's PAP by at least 20 mmHg. Incertain embodiments, the method relates to reducing the patient's PAP byat least 25 mmHg. In some embodiments, the method relates to reducingpulmonary vascular resistance (PVR). In some embodiments, the methodrelate to increasing pulmonary capillary wedge pressure (PCWP). In someembodiments, the method relate to increasing left ventricularend-diastolic pressure (LVEDP).

In certain aspects, the disclosure relates to methods of treating,preventing, or reducing the progression rate and/or severity of one ormore complications of pulmonary hypertension comprising administering toa patient in need thereof an effective amount of a GDF/BMP antagonist(e.g., an antagonist of one or more of activin, GDF8, GDF11, GDF3, BMP6,BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins). In some embodiments, the method relates to treating,preventing, or reducing the progression rate and/or severity of cellproliferation in the pulmonary artery of a pulmonary hypertensionpatient. In some embodiments, the method relates to treating,preventing, or reducing the progression rate and/or severity of smoothmuscle and/or endothelial cells proliferation in the pulmonary artery ofa pulmonary hypertension patient. In some embodiments, the methodrelates to treating, preventing, or reducing the progression rate and/orseverity of angiogenesis in the pulmonary artery of a pulmonaryhypertension patient. In some embodiments, the method relates toincreasing physical activity of a patient having pulmonary hypertension.In some embodiments, the method relates to treating, preventing, orreducing the progression rate and/or severity of dyspnea in a pulmonaryhypertension patient. In some embodiments, the method relates totreating, preventing, or reducing the progression rate and/or severityof chest pain in a pulmonary hypertension patient. In some embodiments,the method relates to treating, preventing, or reducing the progressionrate and/or severity of fatigue in a pulmonary hypertension patient. Insome embodiments, the method relates to treating, preventing, orreducing the progression rate and/or severity of pulmonary fibrosis in apulmonary hypertension patient. In some embodiments, the method relatesto treating, preventing, or reducing the progression rate and/orseverity of fibrosis in a pulmonary hypertension patient. In someembodiments, the method relates to treating, preventing, or reducing theprogression rate and/or severity of pulmonary vascular remodeling in apulmonary hypertension patient. In some embodiments, the method relatesto treating, preventing, or reducing the progression rate and/orseverity of right ventricular hypertrophy in a pulmonary hypertensionpatient.

In certain aspects, the disclosure relates to methods of increasingexercise capacity in a patient having pulmonary hypertension comprisingadministering to a patient in need thereof an effective amount of aGDF/BMP antagonist (e.g., an antagonist of one or more of activin, GDF8,GDF11, GDF3, BMP6, BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, andone or more Smad proteins). Any suitable measure of exercise capacitycan be used. For example, exercise capacity in a 6-minute walk test(6MWT), which measures how far the subject can walk in 6 minutes, i.e.,the 6-minute walk distance (6MWD), is frequently used to assesspulmonary hypertension severity and disease progression. The Borgdyspnea index (BDI) is a numerical scale for assessing perceived dyspnea(breathing discomfort). It measures the degree of breathlessness, forexample, after completion of the 6MWT, where a BDI of 0 indicates nobreathlessness and 10 indicates maximum breathlessness. In someembodiments, the method relates to increasing 6MWD by at least 10 metersin the patient having pulmonary hypertension. In some embodiments, themethod relates to increasing 6MWD by at least 20 meters in the patienthaving pulmonary hypertension. In some embodiments, the method relatesto increasing 6MWD by at least 30 meters in the patient having pulmonaryhypertension. In some embodiments, the method relates to increasing 6MWDby at least 40 meters in the patient having pulmonary hypertension. Insome embodiments, the method relates to increasing 6MWD by at least 50meters in the patient having pulmonary hypertension. In someembodiments, the method relates to increasing 6MWD by at least 60 metersin the patient having pulmonary hypertension. In some embodiments, themethod relates to increasing 6MWD by at least 70 meters in the patienthaving pulmonary hypertension. In some embodiments, the method relatesto increasing 6MWD by at least 80 meters in the patient having pulmonaryhypertension. In some embodiments, the method relates to increasing 6MWDby at least 90 meters in the patient having pulmonary hypertension. Insome embodiments, the method relates to increasing 6MWD by at least 100meters in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 0.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 1 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 1.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 2 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 2.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 3 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 3.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 4 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 4.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 5.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 6 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 6.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 7 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 7.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 8 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 8.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 9 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 9.5 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by at least 3 indexpoints in the patient having pulmonary hypertension. In someembodiments, the method relate to lowering BDI by 10 index points in thepatient having pulmonary hypertension.

Pulmonary hypertension at baseline can be mild, moderate or severe, asmeasured for example by World Health Organization (WHO) functionalclass, which is a measure of disease severity in patients with pulmonaryhypertension. The WHO functional classification is an adaptation of theNew York Heart Association (NYHA) system and is routinely used toqualitatively assess activity tolerance, for example in monitoringdisease progression and response to treatment (Rubin (2004) Chest126:7-10). Four functional classes are recognized in the WHO system:Class I: pulmonary hypertension without resulting limitation of physicalactivity; ordinary physical activity does not cause undue dyspnea orfatigue, chest pain or near syncope; Class II: pulmonary hypertensionresulting in slight limitation of physical activity; patient comfortableat rest; ordinary physical activity causes undue dyspnea or fatigue,chest pain or near syncope; Class III: pulmonary hypertension resultingin marked limitation of physical activity; patient comfortable at rest;less than ordinary activity causes undue dyspnea or fatigue, chest painor near syncope; Class IV: pulmonary hypertension resulting in inabilityto carry out any physical activity without symptoms; patient manifestssigns of right-heart failure; dyspnea and/or fatigue may be present evenat rest; discomfort is increased by any physical activity.

In certain aspects, the disclosure relates to methods of treating,preventing, or reducing the progression rate and/or severity ofpulmonary hypertension (e.g., treating, preventing, or reducing theprogression rate and/or severity of one or more complications ofpulmonary hypertension) comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist (e.g., an antagonistof one or more of activin, GDF8, GDF11, GDF3, BMP6, BMP15, BMP10,ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smad proteins),wherein the patient has Class I, Class II, Class III, or Class IVpulmonary hypertension as recognized by the WHO. In some embodiments,the method relates to a patient that has Class I pulmonary hypertensionas recognized by the WHO. In some embodiments, the method relates to apatient that has Class II pulmonary hypertension as recognized by theWHO. In some embodiments, the method relates to preventing or delayingpatient progression from Class I pulmonary hypertension to Class IIpulmonary hypertension as recognized by the WHO. In some embodiments,the method relates to promoting or increasing patient regression fromClass II pulmonary hypertension to Class I pulmonary hypertension asrecognized by the WHO. In some embodiments, the method relates to apatient that has Class III pulmonary hypertension as recognized by theWHO. In some embodiments, the method relates to preventing or delayingpatient progression from Class II pulmonary hypertension to Class IIIpulmonary hypertension as recognized by the WHO. In some embodiments,the method relates to promoting or increasing patient regression fromClass III pulmonary hypertension to Class II pulmonary hypertension asrecognized by the WHO. In some embodiments, the method relates topromoting or increasing patient regression from Class III pulmonaryhypertension to Class I pulmonary hypertension as recognized by the WHO.In some embodiments, the method relates to a patient that has Class IVpulmonary hypertension as recognized by the WHO. In some embodiments,the method relates to preventing or delaying patient progression fromClass III pulmonary hypertension to Class IV pulmonary hypertension asrecognized by the WHO. In some embodiments, the method relates topromoting or increasing patient regression from Class IV pulmonaryhypertension to Class III pulmonary hypertension as recognized by theWHO. In some embodiments, the method relates to promoting or increasingpatient regression from Class IV pulmonary hypertension to Class IIpulmonary hypertension as recognized by the WHO. In some embodiments,the method relates to promoting or increasing patient regression fromClass IV pulmonary hypertension to Class I pulmonary hypertension asrecognized by the WHO.

There is no known cure for pulmonary hypertension; current methods oftreatment focus on prolonging patient lifespan and enhancing patientquality of life. Current methods of treatment of pulmonary hypertensioninclude administration of: vasodilators such as prostacyclin,epoprostenol, and sildenafil; endothelin receptor antagonists such asbosentan; calcium channel blockers such as amlodipine, diltiazem, andnifedipine; anticoagulants such as warfarin; and diuretics. Treatment ofpulmonary hypertension has also been carried out using oxygen therapy,atrial septostomy, pulmonary thromboendarterectomy, and lung and/orheart transplantation. Each of these methods, however, suffers from oneor multiple drawbacks which may include lack of effectiveness, seriousside effects, low patient compliance, and high cost. In certain aspects,the method relate to treating, preventing, or reducing the progressionrate and/or severity of pulmonary hypertension (e.g., treating,preventing, or reducing the progression rate and/or severity of one ormore complications of pulmonary hypertension) comprising administeringto a patient in need thereof an effective amount of a GDF/BMP antagonist(e.g., an antagonist of one or more of activin, GDF8, GDF11, GDF3, BMP6,BMP15, BMP10, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, and one or more Smadproteins) in combination (e.g., administered at the same time ordifferent times, but generally in such a manner as to achieveoverlapping pharmacological/physiological effects) with one or moreadditional active agents and/or supportive therapies for treatingpulmonary hypertension (e.g., vasodilators such as prostacyclin,epoprostenol, and sildenafil; endothelin receptor antagonists such asbosentan; calcium channel blockers such as amlodipine, diltiazem, andnifedipine; anticoagulants such as warfarin; diuretics; oxygen therapy;atrial septostomy; pulmonary thromboendarterectomy: and lung and/orheart transplantation); BMP9 polypeptides; BMP10 polypeptides;bardoxolone methyl or a derivative thereof; oleanolic acid or derivativethereof.

In certain embodiments, the present disclosure provides methods formanaging a patient that has been treated with, or is a candidate to betreated with, one or more one or more GDF/BMP antagonists of thedisclosure (e.g., ligand traps such as ActRIIA polypeptides, ActRIIBpolypeptides, and GDF Trap polypeptides) by measuring one or morehematologic parameters in the patient. The hematologic parameters may beused to evaluate appropriate dosing for a patient who is a candidate tobe treated with the antagonist of the present disclosure, to monitor thehematologic parameters during treatment, to evaluate whether to adjustthe dosage during treatment with one or more antagonist of thedisclosure, and/or to evaluate an appropriate maintenance dose of one ormore antagonists of the disclosure. If one or more of the hematologicparameters are outside the normal level, dosing with one or more GDF/BMPantagonists may be reduced, delayed or terminated.

Hematologic parameters that may be measured in accordance with themethods provided herein include, for example, red blood cell levels,blood pressure, iron stores, and other agents found in bodily fluidsthat correlate with increased red blood cell levels, using artrecognized methods. Such parameters may be determined using a bloodsample from a patient. Increases in red blood cell levels, hemoglobinlevels, and/or hematocrit levels may cause increases in blood pressure.

In one embodiment, if one or more hematologic parameters are outside thenormal range or on the high side of normal in a patient who is acandidate to be treated with one or more GDF/BMP antagonists, then onsetof administration of the one or more antagonists of the disclosure maybe delayed until the hematologic parameters have returned to a normal oracceptable level either naturally or via therapeutic intervention. Forexample, if a candidate patient is hypertensive or pre-hypertensive,then the patient may be treated with a blood pressure lowering agent inorder to reduce the patient's blood pressure. Any blood pressurelowering agent appropriate for the individual patient's condition may beused including, for example, diuretics, adrenergic inhibitors (includingalpha blockers and beta blockers), vasodilators, calcium channelblockers, angiotensin-converting enzyme (ACE) inhibitors, or angiotensinII receptor blockers. Blood pressure may alternatively be treated usinga diet and exercise regimen. Similarly, if a candidate patient has ironstores that are lower than normal, or on the low side of normal, thenthe patient may be treated with an appropriate regimen of diet and/oriron supplements until the patient's iron stores have returned to anormal or acceptable level. For patients having higher than normal redblood cell levels and/or hemoglobin levels, then administration of theone or more antagonists of the disclosure may be delayed until thelevels have returned to a normal or acceptable level.

In certain embodiments, if one or more hematologic parameters areoutside the normal range or on the high side of normal in a patient whois a candidate to be treated with one or more GDF/BMP antagonists, thenthe onset of administration may not be delayed. However, the dosageamount or frequency of dosing of the one or more antagonists of thedisclosure may be set at an amount that would reduce the risk of anunacceptable increase in the hematologic parameters arising uponadministration of the one or more antagonists of the disclosure.Alternatively, a therapeutic regimen may be developed for the patientthat combines one or more GDF/BMP antagonists with a therapeutic agentthat addresses the undesirable level of the hematologic parameter. Forexample, if the patient has elevated blood pressure, then a therapeuticregimen may be designed involving administration of one or more GDF/BMPantagonist agents and a blood pressure lowering agent. For a patienthaving lower than desired iron stores, a therapeutic regimen may bedeveloped involving one or more GDF/BMP antagonists of the disclosureand iron supplementation.

In one embodiment, baseline parameter(s) for one or more hematologicparameters may be established for a patient who is a candidate to betreated with one or more GDF/BMP antagonists of the disclosure and anappropriate dosing regimen established for that patient based on thebaseline value(s). Alternatively, established baseline parameters basedon a patient's medical history could be used to inform an appropriateantagonist dosing regimen for a patient. For example, if a healthypatient has an established baseline blood pressure reading that is abovethe defined normal range it may not be necessary to bring the patient'sblood pressure into the range that is considered normal for the generalpopulation prior to treatment with the one or more antagonist of thedisclosure. A patient's baseline values for one or more hematologicparameters prior to treatment with one or more GDF/BMP antagonists ofthe disclosure may also be used as the relevant comparative values formonitoring any changes to the hematologic parameters during treatmentwith the one or more antagonists of the disclosure.

In certain embodiments, one or more hematologic parameters are measuredin patients who are being treated with one or more GDF/BMP antagonists.The hematologic parameters may be used to monitor the patient duringtreatment and permit adjustment or termination of the dosing with theone or more antagonists of the disclosure or additional dosing withanother therapeutic agent. For example, if administration of one or moreGDF/BMP antagonists results in an increase in blood pressure, red bloodcell level, or hemoglobin level, or a reduction in iron stores, then thedose of the one or more antagonists of the disclosure may be reduced inamount or frequency in order to decrease the effects of the one or moreantagonists of the disclosure on the one or more hematologic parameters.If administration of one or more GDF/BMP antagonists results in a changein one or more hematologic parameters that is adverse to the patient,then the dosing of the one or more antagonists of the disclosure may beterminated either temporarily, until the hematologic parameter(s) returnto an acceptable level, or permanently. Similarly, if one or morehematologic parameters are not brought within an acceptable range afterreducing the dose or frequency of administration of the one or moreantagonists of the disclosure, then the dosing may be terminated. As analternative, or in addition to, reducing or terminating the dosing withthe one or more antagonists of the disclosure, the patient may be dosedwith an additional therapeutic agent that addresses the undesirablelevel in the hematologic parameter(s), such as, for example, a bloodpressure lowering agent or an iron supplement. For example, if a patientbeing treated with one or more GDF/BMP antagonists has elevated bloodpressure, then dosing with the one or more antagonists of the disclosuremay continue at the same level and a blood-pressure-lowering agent isadded to the treatment regimen, dosing with the one or more antagonistof the disclosure may be reduced (e.g., in amount and/or frequency) anda blood-pressure-lowering agent is added to the treatment regimen, ordosing with the one or more antagonist of the disclosure may beterminated and the patient may be treated with a blood-pressure-loweringagent.

10. Pharmaceutical Compositions

The therapeutic agents described herein (e.g., GDF/BMP antagonists) maybe formulated into pharmaceutical compositions. Pharmaceuticalcompositions for use in accordance with the present disclosure may beformulated in conventional manner using one or more physiologicallyacceptable carriers or excipients. Such formulations will generally besubstantially pyrogen-free, in compliance with most regulatoryrequirements.

In certain embodiments, the therapeutic methods of the disclosureinclude administering the composition systemically, or locally as animplant or device. When administered, the therapeutic composition foruse in this disclosure is in a substantially pyrogen-free, orpyrogen-free, physiologically acceptable form. Therapeutically usefulagents other than the GDF/BMP antagonists which may also optionally beincluded in the composition as described above, may be administeredsimultaneously or sequentially with the subject compounds in the methodsdisclosed herein.

Typically, protein therapeutic agents disclosed herein will beadministered parentally, and particularly intravenously orsubcutaneously. Pharmaceutical compositions suitable for parenteraladministration may comprise one or more GDF/BMP antagonist incombination with one or more pharmaceutically acceptable sterileisotonic aqueous or nonaqueous solutions, dispersions, suspensions oremulsions, or sterile powders which may be reconstituted into sterileinjectable solutions or dispersions just prior to use, which may containantioxidants, buffers, bacteriostats, solutes which render theformulation isotonic with the blood of the intended recipient orsuspending or thickening agents. Examples of suitable aqueous andnonaqueous carriers which may be employed in the pharmaceuticalcompositions of the disclosure include water, ethanol, polyols (such asglycerol, propylene glycol, polyethylene glycol, and the like), andsuitable mixtures thereof, vegetable oils, such as olive oil, andinjectable organic esters, such as ethyl oleate. Proper fluidity can bemaintained, for example, by the use of coating materials, such aslecithin, by the maintenance of the required particle size in the caseof dispersions, and by the use of surfactants.

The compositions and formulations may, if desired, be presented in apack or dispenser device which may contain one or more unit dosage formscontaining the active ingredient. The pack may for example comprisemetal or plastic foil, such as a blister pack. The pack or dispenserdevice may be accompanied by instructions for administration

Further, the composition may be encapsulated or injected in a form fordelivery to a target tissue site. In certain embodiments, compositionsof the present invention may include a matrix capable of delivering oneor more therapeutic compounds (e.g., GDF/BMP antagonists) to a targettissue site, providing a structure for the developing tissue andoptimally capable of being resorbed into the body. For example, thematrix may provide slow release of the GDF/BMP antagonist. Such matricesmay be formed of materials presently in use for other implanted medicalapplications.

The choice of matrix material is based on biocompatibility,biodegradability, mechanical properties, cosmetic appearance andinterface properties. The particular application of the subjectcompositions will define the appropriate formulation. Potential matricesfor the compositions may be biodegradable and chemically defined calciumsulfate, tricalcium phosphate, hydroxyapatite, polylactic acid andpolyanhydrides. Other potential materials are biodegradable andbiologically well defined, such as bone or dermal collagen. Furthermatrices are comprised of pure proteins or extracellular matrixcomponents. Other potential matrices are non-biodegradable andchemically defined, such as sintered hydroxyapatite, bioglass,aluminates, or other ceramics. Matrices may be comprised of combinationsof any of the above mentioned types of material, such as polylactic acidand hydroxyapatite or collagen and tricalcium phosphate. The bioceramicsmay be altered in composition, such as in calcium-aluminate-phosphateand processing to alter pore size, particle size, particle shape, andbiodegradability.

In certain embodiments, methods of the invention can be administered fororally, e.g., in the form of capsules, cachets, pills, tablets, lozenges(using a flavored basis, usually sucrose and acacia or tragacanth),powders, granules, or as a solution or a suspension in an aqueous ornon-aqueous liquid, or as an oil-in-water or water-in-oil liquidemulsion, or as an elixir or syrup, or as pastilles (using an inertbase, such as gelatin and glycerin, or sucrose and acacia) and/or asmouth washes and the like, each containing a predetermined amount of anagent as an active ingredient. An agent may also be administered as abolus, electuary or paste.

In solid dosage forms for oral administration (capsules, tablets, pills,dragees, powders, granules, and the like), one or more therapeuticcompounds of the present invention may be mixed with one or morepharmaceutically acceptable carriers, such as sodium citrate ordicalcium phosphate, and/or any of the following: (1) fillers orextenders, such as starches, lactose, sucrose, glucose, mannitol, and/orsilicic acid; (2) binders, such as, for example, carboxymethylcellulose,alginates, gelatin, polyvinyl pyrrolidone, sucrose, and/or acacia; (3)humectants, such as glycerol; (4) disintegrating agents, such asagar-agar, calcium carbonate, potato or tapioca starch, alginic acid,certain silicates, and sodium carbonate; (5) solution retarding agents,such as paraffin; (6) absorption accelerators, such as quaternaryammonium compounds; (7) wetting agents, such as, for example, cetylalcohol and glycerol monostearate; (8) absorbents, such as kaolin andbentonite clay; (9) lubricants, such a talc, calcium stearate, magnesiumstearate, solid polyethylene glycols, sodium lauryl sulfate, andmixtures thereof; and (10) coloring agents. In the case of capsules,tablets and pills, the pharmaceutical compositions may also comprisebuffering agents. Solid compositions of a similar type may also beemployed as fillers in soft and hard-filled gelatin capsules using suchexcipients as lactose or milk sugars, as well as high molecular weightpolyethylene glycols and the like.

Liquid dosage forms for oral administration include pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups,and elixirs. In addition to the active ingredient, the liquid dosageforms may contain inert diluents commonly used in the art, such as wateror other solvents, solubilizing agents and emulsifiers, such as ethylalcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzylalcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils(in particular, cottonseed, groundnut, corn, germ, olive, castor, andsesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycolsand fatty acid esters of sorbitan, and mixtures thereof. Besides inertdiluents, the oral compositions can also include adjuvants such aswetting agents, emulsifying and suspending agents, sweetening,flavoring, coloring, perfuming, and preservative agents.

Suspensions, in addition to the active compounds, may contain suspendingagents such as ethoxylated isostearyl alcohols, polyoxyethylenesorbitol, and sorbitan esters, microcrystalline cellulose, aluminummetahydroxide, bentonite, agar-agar and tragacanth, and mixturesthereof.

The compositions of the invention may also contain adjuvants, such aspreservatives, wetting agents, emulsifying agents and dispersing agents.Prevention of the action of microorganisms may be ensured by theinclusion of various antibacterial and antifungal agents, for example,paraben, chlorobutanol, phenol sorbic acid, and the like. It may also bedesirable to include isotonic agents, such as sugars, sodium chloride,and the like into the compositions. In addition, prolonged absorption ofthe injectable pharmaceutical form may be brought about by the inclusionof agents which delay absorption, such as aluminum monostearate andgelatin.

It is understood that the dosage regimen will be determined by theattending physician considering various factors which modify the actionof the subject compounds of the disclosure (e.g., GDF/BMP antagonists).The various factors include, but are not limited to, the patient's age,sex, and diet, the severity disease, time of administration, and otherclinical factors. Optionally, the dosage may vary with the type ofmatrix used in the reconstitution and the types of compounds in thecomposition. The addition of other known growth factors to the finalcomposition, may also affect the dosage. Progress can be monitored byperiodic assessment of bone growth and/or repair, for example, X-rays(including DEXA), histomorphometric determinations, and tetracyclinelabeling.

In certain embodiments, the present invention also provides gene therapyfor the in vivo production of GDF/BMP antagonists. Such therapy wouldachieve its therapeutic effect by introduction of the GDF/BMP antagonistpolynucleotide sequences into cells or tissues having the disorders aslisted above. Delivery of GDF/BMP antagonist polynucleotide sequencescan be achieved using a recombinant expression vector such as a chimericvirus or a colloidal dispersion system. Preferred for therapeuticdelivery of GDF/BMP antagonist polynucleotide sequences is the use oftargeted liposomes.

Various viral vectors which can be utilized for gene therapy as taughtherein include adenovirus, herpes virus, vaccinia, or, preferably, anRNA virus such as a retrovirus. Preferably, the retroviral vector is aderivative of a murine or avian retrovirus. Examples of retroviralvectors in which a single foreign gene can be inserted include, but arenot limited to: Moloney murine leukemia virus (MoMuLV), Harvey murinesarcoma virus (HaMuSV), murine mammary tumor virus (MuMTV), and RousSarcoma Virus (RSV). A number of additional retroviral vectors canincorporate multiple genes. All of these vectors can transfer orincorporate a gene for a selectable marker so that transduced cells canbe identified and generated. Retroviral vectors can be madetarget-specific by attaching, for example, a sugar, a glycolipid, or aprotein. Preferred targeting is accomplished by using an antibody. Thoseof skill in the art will recognize that specific polynucleotidesequences can be inserted into the retroviral genome or attached to aviral envelope to allow target specific delivery of the retroviralvector containing the GDF/BMP antagonist. In a preferred embodiment, thevector is targeted to bone or cartilage.

Alternatively, tissue culture cells can be directly transfected withplasmids encoding the retroviral structural genes gag, pol and env, byconventional calcium phosphate transfection. These cells are thentransfected with the vector plasmid containing the genes of interest.The resulting cells release the retroviral vector into the culturemedium.

Another targeted delivery system for GDF/BMP antagonist polynucleotidesis a colloidal dispersion system. Colloidal dispersion systems includemacromolecule complexes, nanocapsules, microspheres, beads, andlipid-based systems including oil-in-water emulsions, micelles, mixedmicelles, and liposomes. The preferred colloidal system of thisinvention is a liposome. Liposomes are artificial membrane vesicleswhich are useful as delivery vehicles in vitro and in vivo. RNA, DNA andintact virions can be encapsulated within the aqueous interior and bedelivered to cells in a biologically active form (see e.g., Fraley, etal., Trends Biochem. Sci., 6:77, 1981). Methods for efficient genetransfer using a liposome vehicle, are known in the art, see e.g.,Mannino, et al., Biotechniques, 6:682, 1988. The composition of theliposome is usually a combination of phospholipids, usually incombination with steroids, especially cholesterol. Other phospholipidsor other lipids may also be used. The physical characteristics ofliposomes depend on pH, ionic strength, and the presence of divalentcations.

Examples of lipids useful in liposome production include phosphatidylcompounds, such as phosphatidylglycerol, phosphatidylcholine,phosphatidylserine, phosphatidylethanolamine, sphingolipids,cerebrosides, and gangliosides. Illustrative phospholipids include eggphosphatidylcholine, dipalmitoylphosphatidylcholine, anddistearoylphosphatidylcholine. The targeting of liposomes is alsopossible based on, for example, organ-specificity, cell-specificity, andorganelle-specificity and is known in the art.

The disclosure provides formulations that may be varied to include acidsand bases to adjust the pH; and buffering agents to keep the pH within anarrow range.

EXEMPLIFICATION

The invention now being generally described, it will be more readilyunderstood by reference to the following examples, which are includedmerely for purposes of illustration of certain embodiments of thepresent invention, and are not intended to limit the invention.

Example 1: ActRIIa-Fc Fusion Proteins

A soluble ActRIIA fusion protein was constructed that has theextracellular domain of human ActRIIa fused to a human or mouse Fcdomain with a minimal linker in between. The constructs are referred toas ActRIIA-hFc and ActRIIA-mFc, respectively.

ActRIIA-hFc is shown below as purified from CHO cell lines (SEQ ID NO:32):

ILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEMEVTQPTSNPVTPKPPTGGGTHTCPPCPAPELLGGPSVFLEPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

The ActRIIA-hFc and ActRIIA-mFc proteins were expressed in CHO celllines. Three different leader sequences were considered:

-   -   (i) Honey bee mellitin (HBML):

(SEQ ID NO: 33) MKFLVNVALVFMVVYISYIYA

-   -   (ii) Tissue plasminogen activator (TPA):

(SEQ ID NO: 34) MDAMKRGLCCVLLLCGAVFVSP

-   -   (iii) Native:

(SEQ ID NO: 35) MGAAAKLAFAVFLISCSSGA.

The selected form employs the TPA leader and has the followingunprocessed amino acid sequence:

(SEQ ID NO: 36) MDAMKRGLCCVLLLCGAVEVSPGAAILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEMEVTQPTSNPVTPKPPTGGGTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGEYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVM HEALHNHYTQKSLSLSPGK

This polypeptide is encoded by the following nucleic acid sequence:

(SEQ ID NO: 37) ATGGATGCAATGAAGAGAGGGCTCTGCTGTGTGCTGCTGCTGTGTGGAGCAGTCTTCGTTTCGCCCGGCGCCGCTATACTTGGTAGATCAGAAACTCAGGAGTGTCTTTTTTTAATGCTAATTGGGAAAAAGACAGAACCAATCAAACTGGTGTTGAACCGTGTTATGGTGACAAAGATAAACGGCGGCATTGTTTTGCTACCTGGAAGAATATTTCTGGTTCCATTGAATAGTGAAACAAGGTTGTTGGCTGGATGATATCAACTGCTATGACAGGACTGATTGTGTAGAAAAAAAAGACAGCCCTGAAGTATATTTCTGTTGCTGTGAGGGCAATATGTGTAATGAAAAGTTTTCTTATTTTCCGGAGATGGAAGTCACACAGCCCACTTCAAATCCAGTTACACCTAAGCCACCCACCGGTGGTGGAACTCACACATGCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAGTCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGAGGAGATGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTATAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGG GTAAATGAGAATTC

Both ActRIIA-hFc and ActRIIA-mFc were remarkably amenable to recombinantexpression. As shown in FIG. 5, the protein was purified as a single,well-defined peak of protein. N-terminal sequencing revealed a singlesequence of -ILGRSETQE (SEQ ID NO: 38). Purification could be achievedby a series of column chromatography steps, including, for example,three or more of the following, in any order: protein A chromatography,Q sepharose chromatography, phenylsepharose chromatography, sizeexclusion chromatography, and cation exchange chromatography. Thepurification could be completed with viral filtration and bufferexchange. The ActRIIA-hFc protein was purified to a purity of >98% asdetermined by size exclusion chromatography and >95% as determined bySDS PAGE.

ActRIIA-hFc and ActRIIA-mFc showed a high affinity for ligands. GDF11 oractivin A were immobilized on a Biacore™ CM5 chip using standardamine-coupling procedure. ActRIIA-hFc and ActRIIA-mFc proteins wereloaded onto the system, and binding was measured. ActRIIA-hFc bound toactivin with a dissociation constant (K_(D)) of 5×10⁻¹² and bound toGDF11 with a K_(D) of 9.96×10⁻⁹. See FIG. 6. Using a similar bindingassay, ActRIIA-hFc was determined to have high to moderate affinity forother TGF-beta superfamily ligands including, for example, activin B,GDF8, BMP6, and BMP10. ActRIIA-mFc behaved similarly.

The ActRIIA-hFc was very stable in pharmacokinetic studies. Rats weredosed with 1 mg/kg, 3 mg/kg, or 10 mg/kg of ActRIIA-hFc protein, andplasma levels of the protein were measured at 24, 48, 72, 144 and 168hours. In a separate study, rats were dosed at 1 mg/kg, 10 mg/kg, or 30mg/kg. In rats, ActRIIA-hFc had an 11-14 day serum half-life, andcirculating levels of the drug were quite high after two weeks (11μg/ml, 110 μg/ml, or 304 μg/ml for initial administrations of 1 mg/kg,10 mg/kg, or 30 mg/kg, respectively.) In cynomolgus monkeys, the plasmahalf-life was substantially greater than 14 days, and circulating levelsof the drug were 25 μg/ml, 304 μg/ml, or 1440 μg/ml for initialadministrations of 1 mg/kg, 10 mg/kg, or 30 mg/kg, respectively.

Example 2: Characterization of an ActRIIA-hFc Protein

ActRIIA-hFc fusion protein was expressed in stably transfected CHO-DUKXB11 cells from a pAID4 vector (SV40 ori/enhancer, CMV promoter), using atissue plasminogen leader sequence of SEQ ID NO: 34. The protein,purified as described above in Example 1, had a sequence of SEQ ID NO:32. The Fc portion is a human IgG1 Fc sequence, as shown in SEQ ID NO:32. Protein analysis reveals that the ActRIIA-hFc fusion protein isformed as a homodimer with disulfide bonding.

The CHO-cell-expressed material has a higher affinity for activin Bligand than that reported for an ActRIIa-hFc fusion protein expressed inhuman 293 cells [see, del Re et al. (2004) J Biol Chem.279(51):53126-53135]. Additionally, the use of the TPA leader sequenceprovided greater production than other leader sequences and, unlikeActRIIA-Fc expressed with a native leader, provided a highly pureN-terminal sequence. Use of the native leader sequence resulted in twomajor species of ActRIIA-Fc, each having a different N-terminalsequence.

Example 3: Alternative ActRIIA-Fc Proteins

A variety of ActRIIA variants that may be used according to the methodsdescribed herein are described in the International Patent Applicationpublished as WO2006/012627 (see e.g., pp. 55-58), incorporated herein byreference in its entirety. An alternative construct may have a deletionof the C-terminal tail (the final 15 amino acids of the extracellulardomain of ActRIIA. The sequence for such a construct is presented below(Fc portion underlined) (SEQ ID NO: 39):

ILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEMTGGGTHTCPPCPAPELLGGPSVFLEPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Example 4: Generation of ActRIIB-Fc Fusion Proteins

Applicants constructed a soluble ActRIIB fusion protein that has theextracellular domain of human ActRIIB fused to a human or mouse Fcdomain with a minimal linker in between. The constructs are referred toas ActRIIB-hFc and ActRIIB-mFc, respectively.

ActRIIB-hFc is shown below as purified from CHO cell lines (SEQ ID NO:40):

GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEVTYEPPPTAPTGGGTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

The ActRIIB-hFc and ActRIIB-mFc proteins were expressed in CHO celllines. Three different leader sequences were considered: (i) Honey beemellitin (HBML), ii) Tissue plasminogen activator (TPA), and (iii)Native:

(SEQ ID NO: 41) MGAAAKLAFAVFLISCSSGA.

The selected form employs the TPA leader and has the followingunprocessed amino acid sequence (SEQ ID NO: 42):

MDAMKRGLCCVLLLCGAVFVSPGASGRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEVTYEPPPTAPTGGGTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMH EALHNHYTQKSLSLSPGK

This polypeptide is encoded by the following nucleic acid sequence (SEQID NO: 43):

A TGGATGCAAT GAAGAGAGGG CTCTGCTGTG TGCTGCTGCTGTGTGGAGCA GTCTTCGTTT CGCCCGGCGC CTCTGGGCGTGGGGAGGCTG AGACACGGGA GTGCATCTAC TACAACGCCAACTGGGAGCT GGAGCGCACC AACCAGAGCG GCCTGGAGCGCTGCGAAGGC GAGCAGGACA AGCGGCTGCA CTGCTACGCCTCCTGGCGCA ACAGCTCTGG CACCATCGAG CTCGTGAAGAAGGGCTGCTG GCTAGATGAC TTCAACTGCT ACGATAGGCAGGAGTGTGTG GCCACTGAGG AGAACCCCCA GGTGTACTTCTGCTGCTGTG AAGGCAACTT CTGCAACGAG CGCTTCACTCATTTGCCAGA GGCTGGGGGC CCGGAAGTCA CGTACGAGCCACCCCCGACA GCCCCCACCG GTGGTGGAAC TCACACATGCCCACCGTGCC CAGCACCTGA ACTCCTGGGG GGACCGTCAGTCTTCCTCTT CCCCCCAAAA CCCAAGGACA CCCTCATGATCTCCCGGACC CCTGAGGTCA CATGCGTGGT GGTGGACGTGAGCCACGAAG ACCCTGAGGT CAAGTTCAAC TGGTACGTGGACGGCGTGGA GGTGCATAAT GCCAAGACAA AGCCGCGGGAGGAGCAGTAC AACAGCACGT ACCGTGTGGT CAGCGTCCTCACCGTCCTGC ACCAGGACTG GCTGAATGGC AAGGAGTACAAGTGCAAGGT CTCCAACAAA GCCCTCCCAG TCCCCATCGAGAAAACCATC TCCAAAGCCA AAGGGCAGCC CCGAGAACCACAGGTGTACA CCCTGCCCCC ATCCCGGGAG GAGATGACCAAGAACCAGGT CAGCCTGACC TGCCTGGTCA AAGGCTTCTATCCCAGCGAC ATCGCCGTGG AGTGGGAGAG CAATGGGCAGCCGGAGAACA ACTACAAGAC CACGCCTCCC GTGCTGGACTCCGACGGCTC CTTCTTCCTC TATAGCAAGC TCACCGTGGACAAGAGCAGG TGGCAGCAGG GGAACGTCTT CTCATGCTCCGTGATGCATG AGGCTCTGCA CAACCACTAC ACGCAGAAGA GCCTCTCCCT GTCTCCGGGT AAATGA

N-terminal sequencing of the CHO-cell-produced material revealed a majorsequence of -GRGEAE (SEQ ID NO: 44). Notably, other constructs reportedin the literature begin with an -SGR . . . sequence.

Purification could be achieved by a series of column chromatographysteps, including, for example, three or more of the following, in anyorder: protein A chromatography, Q sepharose chromatography,phenylsepharose chromatography, size exclusion chromatography, andcation exchange chromatography. The purification could be completed withviral filtration and buffer exchange.

ActRIIB-Fc fusion proteins were also expressed in HEK293 cells and COScells. Although material from all cell lines and reasonable cultureconditions provided protein with muscle-building activity in vivo,variability in potency was observed perhaps relating to cell lineselection and/or culture conditions.

Applicants generated a series of mutations in the extracellular domainof ActRIIB and produced these mutant proteins as soluble fusion proteinsbetween extracellular ActRIIB and an Fc domain. The backgroundActRIIB-Fc fusion has the sequence of SEQ ID NO: 40.

Various mutations, including N- and C-terminal truncations, wereintroduced into the background ActRIIB-Fc protein. Based on the datapresented herien, it is expected that these constructs, if expressedwith a TPA leader, will lack the N-terminal serine. Mutations weregenerated in ActRIIB extracellular domain by PCR mutagenesis. After PCR,fragments were purified through a Qiagen column, digested with SfoI andAgeI and gel purified. These fragments were ligated into expressionvector pAID4 (see WO2006/012627) such that upon ligation it createdfusion chimera with human IgG1. Upon transformation into E. coli DH5alpha, colonies were picked and DNAs were isolated. For murineconstructs (mFc), a murine IgG2a was substituted for the human IgG1.Sequences of all mutants were verified.

All of the mutants were produced in HEK293T cells by transienttransfection. In summary, in a 500 ml spinner, HEK293T cells were set upat 6×10⁵ cells/ml in Freestyle (Invitrogen) media in 250 ml volume andgrown overnight. Next day, these cells were treated with DNA:PEI (1:1)complex at 0.5 ug/ml final DNA concentration. After 4 hrs, 250 ml mediawas added and cells were grown for 7 days. Conditioned media washarvested by spinning down the cells and concentrated.

Mutants were purified using a variety of techniques, including, forexample, a protein A column, and eluted with low pH (3.0) glycinebuffer. After neutralization, these were dialyzed against PBS.

Mutants were also produced in CHO cells by similar methodology. Mutantswere tested in binding assays and/or bioassays described in WO2008/097541 and WO 2006/012627 incorporated by reference herein. In someinstances, assays were performed with conditioned medium rather thanpurified proteins. Additional variations of ActRIIB are described inU.S. Pat. No. 7,842,663.

Applicant generated an ActRIIB(25-131)-hFc fusion protein, whichcomprises the human ActRIIB extracellular domain with N-terminal andC-terminal truncations (residues 25-131 of the native protein SEQ IDNO: 1) fused N-terminally with a TPA leader sequence substituted for thenative ActRIIB leader and C-terminally with a human Fc domain via aminimal linker (three glycine residues) (FIG. 7). A nucleotide sequenceencoding this fusion protein is shown in FIG. 8. Applicants modified thecodons and found a variant nucleic acid encoding the ActRIIB(25-131)-hFcprotein that provided substantial improvement in the expression levelsof initial transformants (FIG. 9).

The mature protein has an amino acid sequence as follows (N-terminusconfirmed by N-terminal sequencing)(SEQ ID NO: 45):

ETRECIYYNA NWELERTNQS GLERCEGEQD KRLHCYASWRNSSGTIELVK KGCWLDDFNC YDRQECVATE ENPQVYFCCCEGNFCNERFT HLPEAGGPEV TYEPPPTGGG THTCPPCPAPELLGGPSVFL FPPKPKDTLM ISRTPEVTCV VVDVSHEDPEVKFNWYVDGV EVHNAKTKPR EEQYNSTYRV VSVLTVLHQDWLNGKEYKCK VSNKALPAPI EKTISKAKGQ PREPQVYTLPPSREEMTKNQ VSLTCLVKGF YPSDIAVEWE SNGQPENNYKTTPPVLDSDG SFFLYSKLTV DKSRWQQGNV FSCSVMHEAL HNHYTQKSLS LSPGK

The expressed molecule was purified using a series of columnchromatography steps, including for example, three or more of thefollowing, in any order: Protein A chromatography, Q sepharosechromatography, phenylsepharose chromatography, size exclusionchromatography and cation exchange chromatography. The purificationcould be completed with viral filtration and buffer exchange.

Affinities of several ligands for ActRIIB(25-131)-hFc and itsfull-length counterpart ActRIIB(20-134)-hFc were evaluated in vitro witha Biacore™ instrument, and the results are summarized in the tablebelow. Kd values were obtained by steady-state affinity fit due to veryrapid association and dissociation of the complex, which preventedaccurate determination of k_(on) and k_(off). ActRIIB(25-131)-hFc bound,for example, activin A, activin B, and GDF11 with high affinity.

Ligand Affinities of ActRIIB-hFc Forms:

Activin A Activin B GDF11 Fusion Construct (e−11) (e−11) (e−11)ActRIIB(20-134)-hFc 1.6 1.2 3.6 ActRIIB(25-131)-hFc 1.8 1.2 3.1

Example 5: Generation of a GDF Trap

A GDF trap was constructed as follows. A polypeptide having a modifiedextracellular domain of ActRIIB (amino acids 20-134 of SEQ ID NO: 1 withan L79D substitution) with greatly reduced activin A binding relative toGDF11 and/or myostatin (as a consequence of a leucine-to-aspartatesubstitution at position 79 in SEQ ID NO:1) was fused to a human ormouse Fc domain with a minimal linker in between. The constructs arereferred to as ActRIIB(L79D 20-134)-hFc and ActRIIB(L79D 20-134)-mFc,respectively. Alternative forms with a glutamate rather than anaspartate at position 79 performed similarly (L79E). Alternative formswith an alanine rather than a valine at position 226 with respect to SEQID NO: 64, below were also generated and performed equivalently in allrespects tested. The aspartate at position 79 (relative to SEQ ID NO: 1)is indicated with double underlining below. The valine at position 226relative to SEQ ID NO: 64 is also indicated by double underlining below.

The GDF trap ActRIIB(L79D 20-134)-hFc is shown below as purified fromCHO cell lines (SEQ ID NO: 46).

GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWDDDENCYDRQECVATEENPQVYFCCCEGNECNERFTHLPEAGGPEVTYEPPPTAPTGGGTHTCPPCPAPELLGGPSVFLEPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

The ActRIIB-derived portion of the GDF trap has an amino acid sequenceset forth below (SEQ ID NO: 47), and that portion could be used as amonomer or as a non-Fc fusion protein as a monomer, dimer, orgreater-order complex.

(SEQ ID NO: 47) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWDDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEA GGPEVTYEPPPTAPT

The GDF trap protein was expressed in CHO cell lines. Three differentleader sequences were considered:

(i) Honey bee melittin (HBML), (ii) Tissue plasminogen activator (TPA),and (iii) Native.

The selected form employs the TPA leader and has the followingunprocessed amino acid sequence:

(SEQ ID NO: 48) MDAMKRGLCCVLLLCGAVEVSPGASGRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWDDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEVTYEPPPTAPTGGGTHTCPPCPAPELLGGPSVFLEPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

This polypeptide is encoded by the following nucleic acid sequence (SEQID NO: 49):

A TGGATGCAAT GAAGAGAGGG CTCTGCTGTG TGCTGCTGCTGTGTGGAGCA GTCTTCGTTT CGCCCGGCGC CTCTGGGCGTGGGGAGGCTG AGACACGGGA GTGCATCTAC TACAACGCCAACTGGGAGCT GGAGCGCACC AACCAGAGCG GCCTGGAGCGCTGCGAAGGC GAGCAGGACA AGCGGCTGCA CTGCTACGCCTCCTGGCGCA ACAGCTCTGG CACCATCGAG CTCGTGAAGAAGGGCTGCTG GGACGATGAC TTCAACTGCT ACGATAGGCAGGAGTGTGTG GCCACTGAGG AGAACCCCCA GGTGTACTTCTGCTGCTGTG AAGGCAACTT CTGCAACGAG CGCTTCACTCATTTGCCAGA GGCTGGGGGC CCGGAAGTCA CGTACGAGCCACCCCCGACA GCCCCCACCG GTGGTGGAAC TCACACATGCCCACCGTGCC CAGCACCTGA ACTCCTGGGG GGACCGTCAGTCTTCCTCTT CCCCCCAAAA CCCAAGGACA CCCTCATGATCTCCCGGACC CCTGAGGTCA CATGCGTGGT GGTGGACGTGAGCCACGAAG ACCCTGAGGT CAAGTTCAAC TGGTACGTGGACGGCGTGGA GGTGCATAAT GCCAAGACAA AGCCGCGGGAGGAGCAGTAC AACAGCACGT ACCGTGTGGT CAGCGTCCTCACCGTCCTGC ACCAGGACTG GCTGAATGGC AAGGAGTACAAGTGCAAGGT CTCCAACAAA GCCCTCCCAG TCCCCATCGAGAAAACCATC TCCAAAGCCA AAGGGCAGCC CCGAGAACCACAGGTGTACA CCCTGCCCCC ATCCCGGGAG GAGATGACCAAGAACCAGGT CAGCCTGACC TGCCTGGTCA AAGGCTTCTATCCCAGCGAC ATCGCCGTGG AGTGGGAGAG CAATGGGCAGCCGGAGAACA ACTACAAGAC CACGCCTCCC GTGCTGGACTCCGACGGCTC CTTCTTCCTC TATAGCAAGC TCACCGTGGACAAGAGCAGG TGGCAGCAGG GGAACGTCTT CTCATGCTCCGTGATGCATG AGGCTCTGCA CAACCACTAC ACGCAGAAGA GCCTCTCCCT GTCTCCGGGT AAATGA

Purification could be achieved by a series of column chromatographysteps, including, for example, three or more of the following, in anyorder: protein A chromatography, Q sepharose chromatography,phenylsepharose chromatography, size exclusion chromatography, andcation exchange chromatography. The purification could be completed withviral filtration and buffer exchange. In an example of a purificationscheme, the cell culture medium is passed over a protein A column,washed in 150 mM Tris/NaCl (pH 8.0), then washed in 50 mM Tris/NaCl (pH8.0) and eluted with 0.1 M glycine, pH 3.0. The low pH eluate is kept atroom temperature for 30 minutes as a viral clearance step. The eluate isthen neutralized and passed over a Q-sepharose ion-exchange column andwashed in 50 mM Tris pH 8.0, 50 mM NaCl, and eluted in 50 mM Tris pH8.0, with an NaCl concentration between 150 mM and 300 mM. The eluate isthen changed into 50 mM Tris pH 8.0, 1.1 M ammonium sulfate and passedover a phenyl sepharose column, washed, and eluted in 50 mM Tris pH 8.0with ammonium sulfate between 150 and 300 mM. The eluate is dialyzed andfiltered for use.

Additional GDF traps (ActRIIB-Fc fusion proteins modified so as toreduce the ratio of activin A binding relative to myostatin or GDF11binding) are described in WO 2008/097541 and WO 2006/012627,incorporated by reference herein.

Example 6: Bioassay for GDF11- and Activin-Mediated Signaling

An A-204 reporter gene assay was used to evaluate the effects ofActRIIB-Fc proteins and GDF traps on signaling by GDF-11 and activin A.Cell line: human rhabdomyosarcoma (derived from muscle). Reportervector: pGL3(CAGA)12 (described in Dennler et al, 1998, EMBO 17:3091-3100). The CAGA12 motif is present in TGF-beta responsive genes(e.g., PAI-1 gene), so this vector is of general use for factorssignaling through SMAD2 and 3.

Day 1: Split A-204 cells into 48-well plate.

Day 2: A-204 cells transfected with 10 ug pGL3(CAGA)12 orpGL3(CAGA)12(10 ug)+pRLCMV (1 μg) and Fugene.

Day 3: Add factors (diluted into medium+0.1% BSA). Inhibitors need to bepreincubated with factors for 1 hr before adding to cells. Six hrslater, cells were rinsed with PBS and lysed.

This is followed by a luciferase assay. In the absence of anyinhibitors, activin A showed 10-fold stimulation of reporter geneexpression and an ED50 ˜2 ng/ml. GDF-11: 16 fold stimulation, ED50: ˜1.5ng/ml.

ActRIIB(20-134) is a potent inhibitor of, for example, activin A, GDF-8,and GDF-11 activity in this assay. As described below, ActRIIB variantswere also tested in this assay.

Example 7: ActRIIB-Fc Variants, Cell-Based Activity

Activity of ActRIIB-Fc proteins and GDF traps was tested in a cell-basedassay as described above. Results are summarized in the table below.Some variants were tested in different C-terminal truncation constructs.As discussed above, truncations of five or fifteen amino acids causedreduction in activity. The GDF traps (L79D and L79E variants) showedsubstantial loss of activin A inhibition while retaining almostwild-type inhibition of GDF11.

Soluble ActRIIB-Fc Binding to GDF11 and Activin A:

Portion of ActRIIB GDF11 Activin ActRIIB-Fc (corresponds to aminoInhibition Inhibition Variations acids of SEQ ID NO: 1) ActivityActivity R64 20-134 +++ +++ (approx. (approx. 10⁻⁸ M K_(I)) 10⁻⁸ MK_(I)) A64 20-134 + + (approx. (approx. 10⁻⁶ M K_(I)) 10⁻⁶ M K_(I)) R6420-129 +++ +++ R64 K74A 20-134 ++++ ++++ R64 A24N 20-134 +++ +++ R64A24N 20-119 ++ ++ R64 A24N K74A 20-119 + + R64 L79P 20-134 + + R64 L79PK74A 20-134 + + R64 L79D 20-134 +++ + R64 L79E 20-134 +++ + R64K 20-134+++ +++ R64K 20-129 +++ +++ R64 P129S 20-134 +++ +++ P130A R64N20-134 + + + Poor activity (roughly 1 × 10⁻⁶ K_(I)) ++ Moderate activity(roughly 1 × 10⁻⁷ K_(I)) +++ Good (wild-type) activity (roughly 1 × 10⁻⁸K_(I)) ++++ Greater than wild-type activity

The A24N variant has activity in the cell-based assay (above) and thatis equivalent to the wild-type molecule. The A24N variant, and any ofthe other variants tested above, may be combined with the GDF trapmolecules, such as the L79D or L79E variants.

Example 8: GDF11 and Activin a Binding

Binding of certain ActRIIB-Fc proteins and GDF traps to ligands wastested in a Biacore™ assay.

The ActRIIB-Fc variants or wild-type protein were captured onto thesystem using an anti-hFc antibody. Ligands were injected and flowed overthe captured receptor proteins. Results are summarized in the tablesbelow.

Ligand-Binding Specificity IIB Variants.

Protein Kon (1/Ms) Koff (1/s) KD (M) GDF11 ActRIIB(20-134)-hFc 1.34e−61.13e−4 8.42e−11 ActRIIB(A24N 20-134)-hFc 1.21e−6 6.35e−5 5.19e−11ActRIIB(L79D 20-134)-hFc  6.7e−5 4.39e−4 6.55e−10 ActRIIB(L79E20-134)-hFc  3.8e−5 2.74e−4 7.16e−10 ActRIIB(R64K 20-134)-hFc 6.77e−52.41e−5 3.56e−11 GDF8 ActRIIB(20-134)-hFc 3.69e−5 3.45e−5 9.35e−11ActRIIB(A24N 20-134)-hFc ActRIIB(L79D 20-134)-hFc 3.85e−5  8.3e−42.15e−9  ActRIIB(L79E 20-134)-hFc 3.74e−5   9e−4 2.41e−9  ActRIIB(R64K20-134)-hFc 2.25e−5 4.71e−5  2.1e−10 ActRIIB(R64K 20-129)-hFc 9.74e−42.09e−4 2.15e−9  ActRIIB(P129S, P130R 1.08e−5  1.8e−4 1.67e−9 20-134)-hFc ActRIIB(K74A 20-134)-hFc  2.8e−5 2.03e−5 7.18e−11 Activin AActRIIB(20-134)-hFc 5.94e6 1.59e−4 2.68e−11 ActRIIB(A24N 20-134)-hFc3.34e6 3.46e−4 1.04e−10 ActRIIB(L79D 20-134)-hFc Low bindingActRIIB(L79E 20-134)-hFc Low binding ActRIIB(R64K 20-134)-hFc 6.82e63.25e−4 4.76e−11 ActRIIB(R64K 20-129)-hFc 7.46e6 6.28e−4 8.41e−11ActRIIB(P129S, P130R 5.02e6 4.17e−4 8.31e−11 20-134)-hFc

These data obtained in a cell-free assay confirm the cell-based assaydata, demonstrating that the A24N variant retains ligand-bindingactivity that is similar to that of the ActRIIB(20-134)-hFc molecule andthat the L79D or L79E molecule retains myostatin and GDF11 binding butshows markedly decreased (non-quantifiable) binding to activin A.

Other variants have been generated and tested, as reported inWO2006/012627 (incorporated herein by reference in its entirety). See,e.g., pp. 59-60, using ligands coupled to the device and flowingreceptor over the coupled ligands. Notably, K74Y, K74F, K74I (andpresumably other hydrophobic substitutions at K74, such as K74L), andD801, cause a decrease in the ratio of activin A (ActA) binding to GDF11binding, relative to the wild-type K74 molecule. A table of data withrespect to these variants is reproduced below:

Soluble ActRIIB-Fc Variants Binding to GDF11 and Activin A (Biacore™Assay)

ActRIIB ActA GDF11 WT (64A) KD = 1.8e−7M KD = 2.6e−7M (+) (+) WT (64R)na KD = 8.6e−8M (+++) +15tail KD ~2.6e−8M KD = 1.9e−8M (+++) (++++)E37A * * R40A − − D54A − * K55A ++ * R56A * * K74A KD = 4.35e−9M  KD =5.3e−9M +++++ +++++ K74Y * −− K74F * −− K74I * −− W78A * * L79A + *D80K * * D80R * * D80A * * D80F * * D80G * * D80M * * D80N * * D80I * −−F82A ++ − * No observed binding −− <⅕ WT binding − ~½ WT binding + WT ++<2× increased binding +++ ~5× increased binding ++++ ~10× increasedbinding +++++ ~40× increased binding

Example 9: Generation of a GDF Trap with Truncated ActRIIB ExtracellularDomain

A GDF trap referred to as ActRIIB(L79D 20-134)-hFc was generated byN-terminal fusion of TPA leader to the ActRIIB extracellular domain(residues 20-134 in SEQ ID NO: 1) containing a leucine-to-aspartatesubstitution (at residue 79 in SEQ ID NO: 1) and C-terminal fusion ofhuman Fc domain with minimal linker (three glycine residues) (FIG. 10;SEQ ID NO: 74). A nucleotide sequence corresponding to this fusionprotein is shown in FIG. 11 (SEQ ID NO: 75, sense strand; and SEQ ID NO:76, antisense strand).

A GDF trap with truncated ActRIIB extracellular domain, referred to asActRIIB(L79D 25-131)-hFc, was generated by N-terminal fusion of TPAleader to truncated extracellular domain (residues 25-131 in SEQ IDNO:1) containing a leucine-to-aspartate substitution (at residue 79 inSEQ ID NO:1) and C-terminal fusion of human Fc domain with minimallinker (three glycine residues) (FIG. 12, SEQ ID NO: 77). The sequenceof the cell purified form of ActRIIB(L79D 25-131)-hFc is presented inFIG. 13 (SEQ ID NO: 78). One nucleotide sequence encoding this fusionprotein is shown in FIG. 15 (SEQ ID NO: 80) along with its complementarysequence (SEQ ID NO: 81), and an alternative nucleotide sequenceencoding exactly the same fusion protein is shown in FIG. 16 (SEQ ID NO:82) and its complementary sequence (SEQ ID NO: 83).

Example 10: Selective Ligand Binding by GDF Trap with Double-TruncatedActRIIB Extracelluar Domain

The affinity of GDF traps and other ActRIIB-hFc proteins for severalligands was evaluated in vitro with a Biacore™ instrument. Results aresummarized in the table below. Kd values were obtained by steady-stateaffinity fit due to the very rapid association and dissociation of thecomplex, which prevented accurate determination of k_(on) and k_(off).

Ligand Selectivity of ActRIIB-hFc Variants:

Activin A Activin B GDF11 Fusion Construct (Kd e−11) (Kd e−11) (Kd e−11)ActRIIB(L79 20-134)-hFc 1.6 1.2 3.6 ActRIIB(L79D 20-134)-hFc 1350.0 78.812.3 ActRIIB(L79 25-131)-hFc 1.8 1.2 3.1 ActRIIB(L79D 25-131)-hFc 2290.062.1 7.4

The GDF trap with a truncated extracellular domain, ActRIIB(L79D25-131)-hFc, equaled or surpassed the ligand selectivity displayed bythe longer variant, ActRIIB(L79D 20-134)-hFc, with pronounced loss ofactivin A binding, partial loss of activin B binding, and nearly fullretention of GDF11 binding compared to ActRIIB-hFc counterparts lackingthe L79D substitution. Note that truncation alone (without L79Dsubstitution) did not alter selectivity among the ligands displayed here[compare ActRIIB(L79 25-131)-hFc with ActRIIB(L79 20-134)-hFc].ActRIIB(L79D 25-131)-hFc also retains strong to intermediate binding tothe Smad 2/3 signaling ligand GDF8 and the Smad 1/5/8 ligands BMP6 andBMP10.

Example 11: GDF Trap Derived from ActRIIB5

Others have reported an alternate, soluble form of ActRIIB (designatedActRIIB5), in which exon 4, including the ActRIIB transmembrane domain,has been replaced by a different C-terminal sequence (see, e.g., WO2007/053775).

The sequence of native human ActRIIB5 without its leader is as follows:

(SEQ ID NO: 50) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEGPWASTTIPSGGPEATAAAGDQGSGALWLCLEGPAHE 

An leucine-to-aspartate substitution, or other acidic substitutions, maybe performed at native position 79 (underlined) as described toconstruct the variant ActRIIB5(L79D), which has the following sequence:

(SEQ ID NO: 51) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWDDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEGPWASTTIPSGGPEATAAAGDQGSGALWLCLEGPAHE 

This variant may be connected to human Fc (double underline) with a TGGGlinker (single underline) to generate a human ActRIIB5(L79D)-hFc fusionprotein with the following sequence:

(SEQ ID NO: 52) GRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWDDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEAGGPEGPWASTTIPSGGPEATAAAGDQGSGALWLCLEGPAHETGGG THTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSV MHEALHNHYTQKSLSLSPGK.

This construct may be expressed in CHO cells.

Example 12: Generation of an ALK4:ActRIIB Heterodimer

An ALK4-Fc:ActRIIB-Fc heteromeric complex was constructed comprising theextracellular domains of human ActRIIB and human ALK4, which are eachseparately fused to an Fc domain with a linker positioned between theextracellular domain and the Fc domain. The individual constructs arereferred to as ActRIIB-Fc fusion polypeptide and ALK4-Fc fusionpolypeptide, respectively, and the sequences for each are providedbelow.

A methodology for promoting formation of ALK4-Fc:ActRIIB-Fc heteromericcomplexes, as opposed to ActRIIB-Fc or ALK4-Fc homodimeric complexes, isto introduce alterations in the amino acid sequence of the Fc domains toguide the formation of asymmetric heteromeric complexes. Many differentapproaches to making asymmetric interaction pairs using Fc domains aredescribed in this disclosure.

In one approach, illustrated in the ActRIIB-Fc and ALK4-Fc polypeptidesequences of SEQ ID NOs: 108 and 110 and SEQ ID Nos: 111 and 113,respectively, one Fc domain is altered to introduce cationic amino acidsat the interaction face, while the other Fc domain is altered tointroduce anionic amino acids at the interaction face. ActRIIB-Fc fusionpolypeptide and ALK4-Fc fusion polypeptide each employ the tissueplasminogen activator (TPA) leader.

The ActRIIB-Fc polypeptide sequence (SEQ ID NO: 108) is shown below:

(SEQ ID NO: 108)   1MDAMKRGLCC VLLLCGAVFV SPGASGRGEA ETRECIYYNA NWELERTNQS  51GLERCEGEQD KRLHCYASWR NSSGTIELVK KGCWLDDFNC YDRQECVATE 101ENPQVYFCCC EGNFCNERFT HLPEAGGPEV TYEPPPTAPT GGGTHTCPPC 151PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV 201DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP 251APIEKTISKA KGQPREPQVY TLPPSRKEMT KNQVSLTCLV KGFYPSDIAV 301EWESNGQPEN NYKTTPPVLK SDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH 351EALHNHYTQK SLSLSPGK

The leader (signal) sequence and linker are underlined. To promoteformation of ALK4-Fc:ActRIIB-Fc heterodimer rather than either of thepossible homodimeric complexes, two amino acid substitutions (replacingacidic amino acids with lysine) can be introduced into the Fc domain ofthe ActRIIB fusion protein as indicated by double underline above. Theamino acid sequence of SEQ ID NO: 108 may optionally be provided withlysine (K) removed from the C-terminus.

This ActRIIB-Fc fusion protein is encoded by the following nucleic acidsequence (SEQ ID NO: 109):

(SEQ ID NO: 109)    1ATGGATGCAA TGAAGAGAGG GCTCTGCTGT GTGCTGCTGC TGTGTGGAGC   51AGTCTTCGTT TCGCCCGGCG CCTCTGGGCG TGGGGAGGCT GAGACACGGG  101AGTGCATCTA CTACAACGCC AACTGGGAGC TGGAGCGCAC CAACCAGAGC  151GGCCTGGAGC GCTGCGAAGG CGAGCAGGAC AAGCGGCTGC ACTGCTACGC  201CTCCTGGCGC AACAGCTCTG GCACCATCGA GCTCGTGAAG AAGGGCTGCT  251GGCTAGATGA CTTCAACTGC TACGATAGGC AGGAGTGTGT GGCCACTGAG  301GAGAACCCCC AGGTGTACTT CTGCTGCTGT GAAGGCAACT TCTGCAACGA  351GCGCTTCACT CATTTGCCAG AGGCTGGGGG CCCGGAAGTC ACGTACGAGC  401CACCCCCGAC AGCCCCCACC GGTGGTGGAA CTCACACATG CCCACCGTGC  451CCAGCACCTG AACTCCTGGG GGGACCGTCA GTCTTCCTCT TCCCCCCAAA  501ACCCAAGGAC ACCCTCATGA TCTCCCGGAC CCCTGAGGTC ACATGCGTGG  551TGGTGGACGT GAGCCACGAA GACCCTGAGG TCAAGTTCAA CTGGTACGTG  601GACGGCGTGG AGGTGCATAA TGCCAAGACA AAGCCGCGGG AGGAGCAGTA  651CAACAGCACG TACCGTGTGG TCAGCGTCCT CACCGTCCTG CACCAGGACT  701GGCTGAATGG CAAGGAGTAC AAGTGCAAGG TCTCCAACAA AGCCCTCCCA  751GCCCCCATCG AGAAAACCAT CTCCAAAGCC AAAGGGCAGC CCCGAGAACC  801ACAGGTGTAC ACCCTGCCCC CATCCCGGAA GGAGATGACC AAGAACCAGG  851TCAGCCTGAC CTGCCTGGTC AAAGGCTTCT ATCCCAGCGA CATCGCCGTG  901GAGTGGGAGA GCAATGGGCA GCCGGAGAAC AACTACAAGA CCACGCCTCC  951CGTGCTGAAG TCCGACGGCT CCTTCTTCCT CTATAGCAAG CTCACCGTGG 1001ACAAGAGCAG GTGGCAGCAG GGGAACGTCT TCTCATGCTC CGTGATGCAT 1051GAGGCTCTGC ACAACCACTA CACGCAGAAG AGCCTCTCCC TGTCTCCGGG 1101 TAAA

A mature ActRIIB-Fc fusion polypeptide (SEQ ID NO: 110) is as follows,and may optionally be provided with lysine (K) removed from theC-terminus.

(SEQ ID NO: 110)   1GRGEAETREC IYYNANWELE RTNQSGLERC EGEQDKRLHC YASWRNSSGT  51IELVKKGCWL DDFNCYDRQE CVATEENPQV YFCCCEGNFC NERFTHLPEA 101GGPEVTYEPP PTAPTGGGTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS 151RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS 201VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPS 251RKEMTKNQVS LTCLVKGFYP SDIAVEWESN GQPENNYKTT PPVLKSDGSF 301FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

A complementary form of ALK4-Fc fusion polypeptide (SEQ ID NO: 111) isas follows:

(SEQ ID NO: 111)   1MDAMKRGLCC VLLLCGAVFV SPGASGPRGV QALLCACTSC LQANYTCETD  51GACMVSIFNL DGMEHHVRTC IPKVELVPAG KPFYCLSSED LRNTHCCYTD 101YCNRIDLRVP SGHLKEPEHP SMWGPVETGG GTHTCPPCPA PELLGGPSVF 151LFPPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP 201REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVSNKALPAP IEKTISKAKG 251QPREPQVYTL PPSREEMTKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY 301DTTPPVLDSD GSFFLYSDLT VDKSRWQQGN VFSCSVMHEA LHNHYTQKSL 351 SLSPG

The leader sequence and linker are underlined. To guide heterodimerformation with the ActRIIB-Fc fusion polypeptide of SEQ ID NOs: 108 and110 above, two amino acid substitutions (replacing lysines with asparticacids) can be introduced into the Fc domain of the ALK4-Fc fusionpolypeptide as indicated by double underline above. The amino acidsequence of SEQ ID NO: 111 may optionally be provided with lysine (K)added at the C-terminus.

This ALK4-Fc fusion protein is encoded by the following nucleic acid(SEQ ID NO: 112):

(SEQ ID NO: 112)    1ATGGATGCAA TGAAGAGAGG GCTCTGCTGT GTGCTGCTGC TGTGTGGAGC   51AGTCTTCGTT TCGCCCGGCG CCTCCGGGCC CCGGGGGGTC CAGGCTCTGC  101TGTGTGCGTG CACCAGCTGC CTCCAGGCCA ACTACACGTG TGAGACAGAT  151GGGGCCTGCA TGGTTTCCAT TTTCAATCTG GATGGGATGG AGCACCATGT  201GCGCACCTGC ATCCCCAAAG TGGAGCTGGT CCCTGCCGGG AAGCCCTTCT  251ACTGCCTGAG CTCGGAGGAC CTGCGCAACA CCCACTGCTG CTACACTGAC  301TACTGCAACA GGATCGACTT GAGGGTGCCC AGTGGTCACC TCAAGGAGCC  351TGAGCACCCG TCCATGTGGG GCCCGGTGGA GACCGGTGGT GGAACTCACA  401CATGCCCACC GTGCCCAGCA CCTGAACTCC TGGGGGGACC GTCAGTCTTC  451CTCTTCCCCC CAAAACCCAA GGACACCCTC ATGATCTCCC GGACCCCTGA  501GGTCACATGC GTGGTGGTGG ACGTGAGCCA CGAAGACCCT GAGGTCAAGT  551TCAACTGGTA CGTGGACGGC GTGGAGGTGC ATAATGCCAA GACAAAGCCG  601CGGGAGGAGC AGTACAACAG CACGTACCGT GTGGTCAGCG TCCTCACCGT  651CCTGCACCAG GACTGGCTGA ATGGCAAGGA GTACAAGTGC AAGGTCTCCA  701ACAAAGCCCT CCCAGCCCCC ATCGAGAAAA CCATCTCCAA AGCCAAAGGG  751CAGCCCCGAG AACCACAGGT GTACACCCTG CCCCCATCCC GGGAGGAGAT  801GACCAAGAAC CAGGTCAGCC TGACCTGCCT GGTCAAAGGC TTCTATCCCA  851GCGACATCGC CGTGGAGTGG GAGAGCAATG GGCAGCCGGA GAACAACTAC  901GACACCACGC CTCCCGTGCT GGACTCCGAC GGCTCCTTCT TCCTCTATAG  951CGACCTCACC GTGGACAAGA GCAGGTGGCA GCAGGGGAAC GTCTTCTCAT 1001GCTCCGTGAT GCATGAGGCT CTGCACAACC ACTACACGCA GAAGAGCCTC 1051TCCCTGTCTC CGGGT

A mature ALK4-Fc fusion protein sequence (SEQ ID NO: 113) is as followsand may optionally be provided with lysine (K) added at the C-terminus.

(SEQ ID NO: 113)   1SGPRGVQALL CACTSCLQAN YTCETDGACM VSIFNLDGME HHVRTCIPKV  51ELVPAGKPFY CLSSEDLRNT HCCYTDYCNR IDLRVPSGHL KEPEHPSMWG 101PVETGGGTHT CPPCPAPELL GGPSVFLFPP KPKDTLMISR TPEVTCVVVD 151VSHEDPEVKF NWYVDGVEVH NAKTKPREEQ YNSTYRVVSV LTVLHQDWLN 201GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVYTLPPSR EEMTKNQVSL 251TCLVKGFYPS DIAVEWESNG QPENNYDTTP PVLDSDGSFF LYSDLTVDKS 301RWQQGNVFSC SVMHEALHNH YTQKSLSLSP G

The ActRIIB-Fc and ALK4-Fc proteins of SEQ ID NO: 110 and SEQ ID NO:113, respectively, may be co-expressed and purified from a CHO cellline, to give rise to a heteromeric complex comprisingALK4-Fc:ActRIIB-Fc.

In another approach to promote the formation of heteromultimer complexesusing asymmetric Fc fusion proteins the Fc domains are altered tointroduce complementary hydrophobic interactions and an additionalintermolecular disulfide bond as illustrated in the ActRIIB-Fc andALK4-Fc polypeptide sequences of SEQ ID NOs: 114 and 115 and SEQ ID Nos:116 and 117, respectively. The ActRIIB-Fc fusion polypeptide and ALK4-Fcfusion polypeptide each employ the tissue plasminogen activator (TPA)leader.

The ActRIIB-Fc polypeptide sequence (SEQ ID NO: 114) is shown below:

(SEQ ID NO: 114)   1MDAMKRGLCC VLLLCGAVFV SPGASGRGEA ETRECIYYNA NWELERTNQS  51GLERCEGEQD KRLHCYASWR NSSGTIELVK KGCWLDDFNC YDRQECVATE 101ENPQVYFCCC EGNFCNERFT HLPEAGGPEV TYEPPPTAPT GGGTHTCPPC 151PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV 201DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP 251APIEKTISKA KGQPREPQVY TLPPCREEMT KNQVSLWCLV KGFYPSDIAV 301EWESNGQPEN NYKTTPPVLD SDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH 351EALHNHYTQK SLSLSPGK

The leader (signal) sequence and linker are underlined. To promoteformation of the ALK4-Fc:ActRIIB-Fc heterodimer rather than either ofthe possible homodimeric complexes, two amino acid substitutions(replacing a serine with a cysteine and a threonine with a trytophan)can be introduced into the Fc domain of the fusion protein as indicatedby double underline above. The amino acid sequence of SEQ ID NO: 114 mayoptionally be provided with lysine (K) removed from the C-terminus.

A mature ActRIIB-Fc fusion polypeptide is as follows:

(SEQ ID NO: 115)   1GRGEAETREC IYYNANWELE RTNQSGLERC EGEQDKRLHC YASWRNSSGT  51IELVKKGCWL DDFNCYDRQE CVATEENPQV YFCCCEGNFC NERFTHLPEA 101GGPEVTYEPP PTAPTGGGTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS 151RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS 201VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPC 251REEMTKNQVS LWCLVKGFYP SDIAVEWESN GQPENNYKTT PPVLDSDGSF 301FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

A complementary form of ALK4-Fc fusion polypeptide (SEQ ID NO: 116) isas follows and may optionally be provided with lysine (K) removed fromthe C-terminus.

(SEQ ID NO: 116)   1MDAMKRGLCC VLLLCGAVFV SPGASGPRGV QALLCACTSC LQANYTCETD  51GACMVSIFNL DGMEHHVRTC IPKVELVPAG KPFYCLSSED LRNTHCCYTD 101YCNRIDLRVP SGHLKEPEHP SMWGPVETGG GTHTCPPCPA PELLGGPSVF 151LFPPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP 201REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVSNKALPAP IEKTISKAKG 251QPREPQVCTL PPSREEMTKN QVSLSCAVKG FYPSDIAVEW ESNGQPENNY 301KTTPPVLDSD GSFFLVSKLT VDKSRWQQGN VFSCSVMHEA LHNHYTQKSL 351 SLSPGK

The leader sequence and the linker are underlined. To guide heterodimerformation with the ActRIIB-Fc fusion polypeptide of SEQ ID NOs: 114 and115 above, four amino acid substitutions can be introduced into the Fcdomain of the ALK4 fusion polypeptide as indicated by double underlineabove. The amino acid sequence of SEQ ID NO: 116 may optionally beprovided with lysine (K) removed from the C-terminus.

A mature ALK4-Fc fusion protein sequence is as follows and mayoptionally be provided with lysine (K) removed from the C-terminus.

(SEQ ID NO: 117)   1SGPRGVQALL CACTSCLQAN YTCETDGACM VSIFNLDGME HHVRTCIPKV  51ELVPAGKPFY CLSSEDLRNT HCCYTDYCNR IDLRVPSGHL KEPEHPSMWG 101PVETGGGTHT CPPCPAPELL GGPSVFLFPP KPKDTLMISR TPEVTCVVVD 151VSHEDPEVKF NWYVDGVEVH NAKTKPREEQ YNSTYRVVSV LTVLHQDWLN 201GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVCTLPPSR EEMTKNQVSL 251SCAVKGFYPS DIAVEWESNG QPENNYKTTP PVLDSDGSFF LVSKLTVDKS 301RWQQGNVFSC SVMHEALHNH YTQKSLSLSP GK

ActRIIB-Fc and ALK4-Fc proteins of SEQ ID NO: 115 and SEQ ID NO: 117respectively, may be co-expressed and purified from a CHO cell line, togive rise to a heteromeric complex comprising ALK4-Fc:ActRIIB-Fc.

Purification of various ALK4-Fc:ActRIIB-Fc complexes could be achievedby a series of column chromatography steps, including, for example,three or more of the following, in any order: protein A chromatography,Q sepharose chromatography, phenylsepharose chromatography, sizeexclusion chromatography, and cation exchange chromatography. Thepurification could be completed with viral filtration and bufferexchange.

In another approach to promote the formation of heteromultimer complexesusing asymmetric Fc fusion proteins, the Fc domains are altered tointroduce complementary hydrophobic interactions, an additionalintermolecular disulfide bond, and electrostatic differences between thetwo Fc domains for facilitating purification based on net molecularcharge, as illustrated in the ActRIIB-Fc and ALK4-Fc polypeptidesequences of SEQ ID NOs: 118-121 and 122-125, respectively. TheActRIIB-Fc fusion polypeptide and ALK4-Fc fusion polypeptide each employthe tissue plasminogen activator (TPA) leader).

The ActRIIB-Fc polypeptide sequence (SEQ ID NO: 118) is shown below:

(SEQ ID NO: 118)   1MDAMKRGLCC VLLLCGAVFV SPGASGRGEA ETRECIYYNA NWELERTNQS  51GLERCEGEQD KRLHCYASWR NSSGTIELVK KGCWLDDFNC YDRQECVATE 101ENPQVYFCCC EGNFCNERFT HLPEAGGPEV TYEPPPTAPT GGGTHTCPPC 151PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV 201DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP 251APIEKTISKA KGQPREPQVY TLPPCREEMT ENQVSLWCLV KGFYPSDIAV 301EWESNGQPEN NYKTTPPVLD SDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH 351 EALHNHYTQDSLSLSPG

The leader sequence and linker are underlined. To promote formation ofthe ALK4-Fc:ActRIIB-Fc heterodimer rather than either of the possiblehomodimeric complexes, two amino acid substitutions (replacing a serinewith a cysteine and a threonine with a trytophan) can be introduced intothe Fc domain of the fusion protein as indicated by double underlineabove. To facilitate purification of the ALK4-Fc:ActRIIB-Fc heterodimer,two amino acid substitutions (replacing lysines with acidic amino acids)can also be introduced into the Fc domain of the fusion protein asindicated by double underline above. The amino acid sequence of SEQ IDNO: 118 may optionally be provided with a lysine added at theC-terminus.

This ActRIIB-Fc fusion protein is encoded by the following nucleic acid(SEQ ID NO: 119):

(SEQ ID NO: 119)    1ATGGATGCAA TGAAGAGAGG GCTCTGCTGT GTGCTGCTGC TGTGTGGAGC   51AGTCTTCGTT TCGCCCGGCG CCTCTGGGCG TGGGGAGGCT GAGACACGGG  101AGTGCATCTA CTACAACGCC AACTGGGAGC TGGAGCGCAC CAACCAGAGC  151GGCCTGGAGC GCTGCGAAGG CGAGCAGGAC AAGCGGCTGC ACTGCTACGC  201CTCCTGGCGC AACAGCTCTG GCACCATCGA GCTCGTGAAG AAGGGCTGCT  251GGCTAGATGA CTTCAACTGC TACGATAGGC AGGAGTGTGT GGCCACTGAG  301GAGAACCCCC AGGTGTACTT CTGCTGCTGT GAAGGCAACT TCTGCAACGA  351GCGCTTCACT CATTTGCCAG AGGCTGGGGG CCCGGAAGTC ACGTACGAGC  401CACCCCCGAC AGCCCCCACC GGTGGTGGAA CTCACACATG CCCACCGTGC  451CCAGCACCTG AACTCCTGGG GGGACCGTCA GTCTTCCTCT TCCCCCCAAA  501ACCCAAGGAC ACCCTCATGA TCTCCCGGAC CCCTGAGGTC ACATGCGTGG  551TGGTGGACGT GAGCCACGAA GACCCTGAGG TCAAGTTCAA CTGGTACGTG  601GACGGCGTGG AGGTGCATAA TGCCAAGACA AAGCCGCGGG AGGAGCAGTA  651CAACAGCACG TACCGTGTGG TCAGCGTCCT CACCGTCCTG CACCAGGACT  701GGCTGAATGG CAAGGAGTAC AAGTGCAAGG TCTCCAACAA AGCCCTCCCA  751GCCCCCATCG AGAAAACCAT CTCCAAAGCC AAAGGGCAGC CCCGAGAACC  801ACAGGTGTAC ACCCTGCCCC CATGCCGGGA GGAGATGACC GAGAACCAGG  851TCAGCCTGTG GTGCCTGGTC AAAGGCTTCT ATCCCAGCGA CATCGCCGTG  901GAGTGGGAGA GCAATGGGCA GCCGGAGAAC AACTACAAGA CCACGCCTCC  951CGTGCTGGAC TCCGACGGCT CCTTCTTCCT CTATAGCAAG CTCACCGTGG 1001ACAAGAGCAG GTGGCAGCAG GGGAACGTCT TCTCATGCTC CGTGATGCAT 1051GAGGCTCTGC ACAACCACTA CACGCAGGAC AGCCTCTCCC TGTCTCCGGG 1101 T

The mature ActRIIB-Fc fusion polypeptide is as follows (SEQ ID NO: 120)and may optionally be provided with a lysine added to the C-terminus.

(SEQ ID NO: 120)   1GRGEAETREC IYYNANWELE RTNQSGLERC EGEQDKRLHC YASWRNSSGT  51IELVKKGCWL DDFNCYDRQE CVATEENPQV YFCCCEGNFC NERFTHLPEA 101GGPEVTYEPP PTAPTGGGTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS 151RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS 201VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPC 251REEMTENQVS LWCLVKGFYP SDIAVEWESN GQPENNYKTT PPVLDSDGSF 301FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQDSLSLS PG

This ActRIIB-Fc fusion polypeptide is encoded by the following nucleicacid (SEQ ID NO: 121):

(SEQ ID NO: 121)    1GGGCGTGGGG AGGCTGAGAC ACGGGAGTGC ATCTACTACA ACGCCAACTG   51GGAGCTGGAG CGCACCAACC AGAGCGGCCT GGAGCGCTGC GAAGGCGAGC  101AGGACAAGCG GCTGCACTGC TACGCCTCCT GGCGCAACAG CTCTGGCACC  151ATCGAGCTCG TGAAGAAGGG CTGCTGGCTA GATGACTTCA ACTGCTACGA  201TAGGCAGGAG TGTGTGGCCA CTGAGGAGAA CCCCCAGGTG TACTTCTGCT  251GCTGTGAAGG CAACTTCTGC AACGAGCGCT TCACTCATTT GCCAGAGGCT  301GGGGGCCCGG AAGTCACGTA CGAGCCACCC CCGACAGCCC CCACCGGTGG  351TGGAACTCAC ACATGCCCAC CGTGCCCAGC ACCTGAACTC CTGGGGGGAC  401CGTCAGTCTT CCTCTTCCCC CCAAAACCCA AGGACACCCT CATGATCTCC  451CGGACCCCTG AGGTCACATG CGTGGTGGTG GACGTGAGCC ACGAAGACCC  501TGAGGTCAAG TTCAACTGGT ACGTGGACGG CGTGGAGGTG CATAATGCCA  551AGACAAAGCC GCGGGAGGAG CAGTACAACA GCACGTACCG TGTGGTCAGC  601GTCCTCACCG TCCTGCACCA GGACTGGCTG AATGGCAAGG AGTACAAGTG  651CAAGGTCTCC AACAAAGCCC TCCCAGCCCC CATCGAGAAA ACCATCTCCA  701AAGCCAAAGG GCAGCCCCGA GAACCACAGG TGTACACCCT GCCCCCATGC  751CGGGAGGAGA TGACCGAGAA CCAGGTCAGC CTGTGGTGCC TGGTCAAAGG  801CTTCTATCCC AGCGACATCG CCGTGGAGTG GGAGAGCAAT GGGCAGCCGG  851AGAACAACTA CAAGACCACG CCTCCCGTGC TGGACTCCGA CGGCTCCTTC  901TTCCTCTATA GCAAGCTCAC CGTGGACAAG AGCAGGTGGC AGCAGGGGAA  951CGTCTTCTCA TGCTCCGTGA TGCATGAGGC TCTGCACAAC CACTACACGC 1001AGGACAGCCT CTCCCTGTCT CCGGGT

The complementary form of ALK4-Fc fusion polypeptide (SEQ ID NO: 122) isas follows and may optionally be provided with lysine removed from theC-terminus.

(SEQ ID NO: 122)   1MDAMKRGLCC VLLLCGAVFV SPGASGPRGV QALLCACTSC LQANYTCETD  51GACMVSIFNL DGMEHHVRTC IPKVELVPAG KPFYCLSSED LRNTHCCYTD 101YCNRIDLRVP SGHLKEPEHP SMWGPVETGG GTHTCPPCPA PELLGGPSVF 151LFPPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP 201REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVSNKALPAP IEKTISKAKG 251QPREPQVCTL PPSREEMTKN QVSLSCAVKG FYPSDIAVEW ESRGQPENNY 301 KTTPPVLDSRGSFFLVSKLT VDKSRWQQGN VFSCSVMHEA LHNHYTQKSL 351 SLSPGK

The leader sequence and the linker are underlined. To guide heterodimerformation with the ActRIIB-Fc fusion polypeptide of SEQ ID NOs: 118 and120 above, four amino acid substitutions (replacing a tyrosine with acysteine, a threonine with a serine, a leucine with an alanine, and atyrosine with a valine) can be introduced into the Fc domain of the ALK4fusion polypeptide as indicated by double underline above. To facilitatepurification of the ALK4-Fc:ActRIIB-Fc heterodimer, two amino acidsubstitutions (replacing an asparagine with an arginine and an aspartatewith an arginine) can also be introduced into the Fc domain of theALK4-Fc fusion polypeptide as indicated by double underline above. Theamino acid sequence of SEQ ID NO: 122 may optionally be provided withlysine removed from the C-terminus.

This ALK4-Fc fusion polypeptide is encoded by the following nucleic acid(SEQ ID NO: 123):

(SEQ ID NO: 123)    1ATGGATGCAA TGAAGAGAGG GCTCTGCTGT GTGCTGCTGC TGTGTGGAGC   51AGTCTTCGTT TCGCCCGGCG CCTCCGGGCC CCGGGGGGTC CAGGCTCTGC  101TGTGTGCGTG CACCAGCTGC CTCCAGGCCA ACTACACGTG TGAGACAGAT  151GGGGCCTGCA TGGTTTCCAT TTTCAATCTG GATGGGATGG AGCACCATGT  201GCGCACCTGC ATCCCCAAAG TGGAGCTGGT CCCTGCCGGG AAGCCCTTCT  251ACTGCCTGAG CTCGGAGGAC CTGCGCAACA CCCACTGCTG CTACACTGAC  301TACTGCAACA GGATCGACTT GAGGGTGCCC AGTGGTCACC TCAAGGAGCC  351TGAGCACCCG TCCATGTGGG GCCCGGTGGA GACCGGTGGT GGAACTCACA  401CATGCCCACC GTGCCCAGCA CCTGAACTCC TGGGGGGACC GTCAGTCTTC  451CTCTTCCCCC CAAAACCCAA GGACACCCTC ATGATCTCCC GGACCCCTGA  501GGTCACATGC GTGGTGGTGG ACGTGAGCCA CGAAGACCCT GAGGTCAAGT  551TCAACTGGTA CGTGGACGGC GTGGAGGTGC ATAATGCCAA GACAAAGCCG  601CGGGAGGAGC AGTACAACAG CACGTACCGT GTGGTCAGCG TCCTCACCGT  651CCTGCACCAG GACTGGCTGA ATGGCAAGGA GTACAAGTGC AAGGTCTCCA  701ACAAAGCCCT CCCAGCCCCC ATCGAGAAAA CCATCTCCAA AGCCAAAGGG  751CAGCCCCGAG AACCACAGGT GTGCACCCTG CCCCCATCCC GGGAGGAGAT  801GACCAAGAAC CAGGTCAGCC TGTCCTGCGC CGTCAAAGGC TTCTATCCCA  851GCGACATCGC CGTGGAGTGG GAGAGCCGCG GGCAGCCGGA GAACAACTAC  901AAGACCACGC CTCCCGTGCT GGACTCCCGC GGCTCCTTCT TCCTCGTGAG  951CAAGCTCACC GTGGACAAGA GCAGGTGGCA GCAGGGGAAC GTCTTCTCAT 1001GCTCCGTGAT GCATGAGGCT CTGCACAACC ACTACACGCA GAAGAGCCTC 1051TCCCTGTCTC CGGGTAAA

The mature ALK4-Fc fusion polypeptide sequence is as follows (SEQ ID NO:124) and may optionally be provided with lysine removed from theC-terminus.

(SEQ ID NO: 124)   1SGPRGVQALL CACTSCLQAN YTCETDGACM VSIFNLDGME HHVRTCIPKV  51ELVPAGKPFY CLSSEDLRNT HCCYTDYCNR IDLRVPSGHL KEPEHPSMWG 101PVETGGGTHT CPPCPAPELL GGPSVFLFPP KPKDTLMISR TPEVTCVVVD 151VSHEDPEVKF NWYVDGVEVH NAKTKPREEQ YNSTYRVVSV LTVLHQDWLN 201GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVCTLPPSR EEMTKNQVSL 251SCAVKGFYPS DIAVEWESRG QPENNYKTTP PVLDSRGSFF LVSKLTVDKS 301RWQQGNVFSC SVMHEALHNH YTQKSLSLSP GK

This ALK4-Fc fusion polypeptide is encoded by the following nucleic acid(SEQ ID NO: 125):

(SEQ ID NO: 125)   1TCCGGGCCCC GGGGGGTCCA GGCTCTGCTG TGTGCGTGCA CCAGCTGCCT  51CCAGGCCAAC TACACGTGTG AGACAGATGG GGCCTGCATG GTTTCCATTT 101TCAATCTGGA TGGGATGGAG CACCATGTGC GCACCTGCAT CCCCAAAGTG 151GAGCTGGTCC CTGCCGGGAA GCCCTTCTAC TGCCTGAGCT CGGAGGACCT 201GCGCAACACC CACTGCTGCT ACACTGACTA CTGCAACAGG ATCGACTTGA 251GGGTGCCCAG TGGTCACCTC AAGGAGCCTG AGCACCCGTC CATGTGGGGC 301CCGGTGGAGA CCGGTGGTGG AACTCACACA TGCCCACCGT GCCCAGCACC 351TGAACTCCTG GGGGGACCGT CAGTCTTCCT CTTCCCCCCA AAACCCAAGG 401ACACCCTCAT GATCTCCCGG ACCCCTGAGG TCACATGCGT GGTGGTGGAC 451GTGAGCCACG AAGACCCTGA GGTCAAGTTC AACTGGTACG TGGACGGCGT 501GGAGGTGCAT AATGCCAAGA CAAAGCCGCG GGAGGAGCAG TACAACAGCA 551CGTACCGTGT GGTCAGCGTC CTCACCGTCC TGCACCAGGA CTGGCTGAAT 601GGCAAGGAGT ACAAGTGCAA GGTCTCCAAC AAAGCCCTCC CAGCCCCCAT 651CGAGAAAACC ATCTCCAAAG CCAAAGGGCA GCCCCGAGAA CCACAGGTGT 701GCACCCTGCC CCCATCCCGG GAGGAGATGA CCAAGAACCA GGTCAGCCTG 751TCCTGCGCCG TCAAAGGCTT CTATCCCAGC GACATCGCCG TGGAGTGGGA 801GAGCCGCGGG CAGCCGGAGA ACAACTACAA GACCACGCCT CCCGTGCTGG 851ACTCCCGCGG CTCCTTCTTC CTCGTGAGCA AGCTCACCGT GGACAAGAGC 901AGGTGGCAGC AGGGGAACGT CTTCTCATGC TCCGTGATGC ATGAGGCTCT 951GCACAACCAC TACACGCAGA AGAGCCTCTC CCTGTCTCCG GGTAAA

ActRIIB-Fc and ALK4-Fc proteins of SEQ ID NO: 120 and SEQ ID NO: 124,respectively, may be co-expressed and purified from a CHO cell line, togive rise to a heteromeric complex comprising ALK4-Fc:ActRIIB-Fc.

Purification of various ALK4-Fc:ActRIIB-Fc complexes could be achievedby a series of column chromatography steps, including, for example,three or more of the following, in any order: protein A chromatography,Q sepharose chromatography, phenylsepharose chromatography, sizeexclusion chromatography, cation exchange chromatography, epitope-basedaffinity chromatography (e.g., with an antibody or functionallyequivalent ligand directed against an epitope on ALK4 or ActRIIB), andmultimodal chromatography (e.g., with resin containing bothelectrostatic and hydrophobic ligands). The purification could becompleted with viral filtration and buffer exchange.

Example 13. Ligand Binding Profile of ALK4-Fc:ActRIIB-Fc HeterodimerCompared to ActRIIB-Fc Homodimer and ALK4-Fc Homodimer

A Biacore™-based binding assay was used to compare ligand bindingselectivity of the ALK4-Fc:ActRIIB-Fc heterodimeric complex describedabove with that of ActRIIB-Fc and ALK4-Fc homodimer complexes. TheALK4-Fc:ActRIIB-Fc heterodimer, ActRIIB-Fc homodimer, and ALK4-Fchomodimer were independently captured onto the system using an anti-Fcantibody. Ligands were injected and allowed to flow over the capturedreceptor protein. Results are summarized in the table below, in whichligand off-rates (k_(d)) most indicative of effective ligand traps aredenoted by gray shading.

These comparative binding data demonstrate that ALK4-Fc:ActRIIB-Fcheterodimer has an altered binding profile/selectivity relative toeither ActRIIB-Fc or ALK4-Fc homodimers. ALK4-Fc:ActRIIB-Fc heterodimerdisplays enhanced binding to activin B compared with either homodimer,retains strong binding to activin A, GDF8, and GDF11 as observed withActRIIB-Fc homodimer, and exhibits substantially reduced binding toBMP9, BMP10, and GDF3. In particular, BMP9 displays low or no observableaffinity for ALK4-Fc:ActRIIB-Fc heterodimer, whereas this ligand bindsstrongly to ActRIIB-Fc homodimer. Like the ActRIIB-Fc homodimer, theheterodimer retains intermediate-level binding to BMP6. See FIG. 19.

In addition, an A-204 Reporter Gene Assay was used to evaluate theeffects of ALK4-Fc:ActRIIB-Fc heterodimer and ActRIIB-Fc:ActRIIB-Fchomodimer on signaling by activin A, activin B, GDF11, GDF8, BMP10, andBMP9. Cell line: Human Rhabdomyosarcoma (derived from muscle). Reportervector: pGL3(CAGA)12 (as described in Dennler et al, 1998, EMBO 17:3091-3100). The CAGA12 motif is present in TGFβ responsive genes (PAI-1gene), so this vector is of general use for factors signaling throughSmad2 and 3. An exemplary A-204 Reporter Gene Assay is outlined below.

-   -   Day 1: Split A-204 cells into 48-well plate.    -   Day 2: A-204 cells transfected with 10 ug pGL3(CAGA)12 or        pGL3(CAGA)12(10 ug)+pRLCMV (1 ug) and Fugene.    -   Day 3: Add factors (diluted into medium+0.1% BSA). Inhibitors        need to be pre-incubated with Factors for about one hr before        adding to cells. About six hrs later, cells are rinsed with PBS        and then lysed.

Following the above steps, a Luciferase assay was performed.

Both the ALK4-Fc:ActRIIB-Fc heterodimer and ActRIIB-Fc:ActRIIB-Fchomodimer were determined to be potent inhibitors of activin A, activinB, GDF11, and GDF8 in this assay. In particular, as can be seen in thecomparative homodimer/heterodimer IC₅₀ data illustrated in FIG. 19,ALK4-Fc:ActRIIB-Fc heterodimer inhibits activin A, activin B, GDF8, andGDF11 signaling pathways similarly to the ActRIIB-Fc:ActRIIB-Fchomodimer. However, ALK4-Fc:ActRIIB-Fc heterodimer inhibition of BMP9and BMP10 signaling pathways is significantly reduced compared to theActRIIB-Fc:ActRIIB-Fc homodimer. This data is consistent with theabove-discussed binding data in which it was observed that both theALK4-Fc:ActRIIB-Fc heterodimer and ActRIIB-Fc:ActRIIB-Fc homodimerdisplay strong binding to activin A, activin B, GDF8, and GDF11, butBMP10 and BMP9 have significantly reduced affinity for theALK4-Fc:ActRIIB-Fc heterodimer compared to the ActRIIB-Fc:ActRIIB-Fchomodimer.

Together, these data therefore demonstrate that ALK4-Fc:ActRIIB-Fcheterodimer is a more selective antagonist of activin A, activin B,GDF8, and GDF11 compared to ActRIIB-Fc homodimer. Accordingly, anALK4-Fc:ActRIIB-Fc heterodimer will be more useful than an ActRIIB-Fchomodimer in certain applications where such selective antagonism isadvantageous. Examples include therapeutic applications where it isdesirable to retain antagonism of one or more of activin A, activin B,activin AC, GDF8, and GDF11 but minimize antagonism of one or more ofBMP9, BMP10, GDF3, and BMP6.

Example 14: Effects of an ActRII Polypeptide and ALK4:ActRIIBHeterodimer on Pulmonary Hypertension in a Monocrotaline Rat Model

The effects of an ActRIIA-mFc fusion protein (ActRIIA-mFc homodimer asdescribed in Example 1), an ALK4-Fc-ActRIIB-Fc heterodimer (as describedin Examples 12 and 13), and sildenafil (a phosphodiesterase-5 inhibitorapproved for the treatment of PAH) were examined in a rat model ofpulmonary arterial hypertension (PAH). In this model, Sprague Dawleyrats received a subcutaneous injection of monocrotaline (MCT) to inducePAH 24 hours prior to start of therapy.

Rats were separated into different treatment groups (10 mice pergroup): 1) treatment with MCT (60 mg/kg administered i.p. as a singledose at day 1 of study) and Tris buffered saline (i.p. as 1 ml/kg, everythree days) (vehicle treatment group), 2) treatment with an ActRIIA-mFcpolypeptide (10 mg/kg administered i.p. every three days) and MCT (60mg/kg administered i.p. as a single dose at day 1 of study), 3)treatment with an ALK4-Fc:ActRIIB-Fc heterodimer (10 mg/kg administeredi.p. every three days) and MCT (60 mg/kg administered i.p. as a singledose at day 1 of study), 4) treatment with sildenafil (30 mg/kgadministered orally twice daily) and MCT (60 mg/kg administered i.p. asa single dose at day 1 of study), and 5) control rats (Tris bufferedsaline administered i.p. as 1 ml/kg, every three days). Rats weretreated for 28 days. Body weights were recorded prior to first dose onDay 1 and then weekly throughout the study.

On day 28, rats were anesthetized by an intraperitoneal injection ofketamine/xylazine (80/10 mg/kg). An incision was made in the neck, and ajugular vein was isolated and ligated anteriorly. A fluid-filledpressure catheter was introduced into the right jugular vein to measurepulmonary artery pressure (PAP). Another incision was made in theinguinal region, and femoral artery was isolated and ligated anteriorly.A Millar pressure catheter was introduced into a femoral artery tomeasure systolic arterial pressure, diastolic pressure, and heart rate.Mean arterial pressure and right PAP were monitored using the NotocordHEM (Croissy sur Seine, Frnace) v3.5 data capture system forapproximately 5-10 minutes until stable measurements were obtained.During the measurements, rats were maintained at approximately 37° C. ona heating pad and body temperature was monitored throughout theprocedure with a rectal temperature probe. At the conclusion of theprocedure, rats were euthanized, and the hearts and lungs were removed.The entire heart was weighed. Next, the atria were removed and the leftventricle with septum (LV+S) was separated from the right ventricle(RV). The ventricles were weighed separately. Hypertrophy was assessed,in part, by calculating RV/LV+S. The lungs were also weighed.

Compared to control animals, monocrotaline treated rats (vehicletreatment group) were observed to have decreased body weight, elevatedPAP, right heart hypertrophy, and increased lung weight, indicatingestablishment of PAH. Sildenafil treated rats did not have anyimprovement in body weight compared to monocrotaline treated rats.However, sildenafil treatment did reduce elevated PAP by 30%, decreaseright heart hypertrophy by 18.5%, and decrease lung weight by 10%compared to monocrotaline treated rats. Surprisingly, bothALK4-Fc:ActRIIB-Fc and ActRIIA-mFc were found have significantly greatereffects in treating PAH in this model compared to sildenafil. Forexample, ALK4-Fc:ActRIIB-Fc treatment resulted in improvement in bodyweight (+5.1%), reduced elevated PAP by 44.6%, decreased right hearthypertrophy by 39.6%, and decreased lung weight by 19.0%. WhileActRIIA-mFc treatment did not show improvement in body weight, it hadsignificant effects in treating other complications of PAH. For example,ActRIIA-Fc treatment resulted in a reduction of elevated PAP by 68%,decreased right heart hypertrophy by 47.1%, and decreased lung weight by18.4%.

Similar trends were observed on vessel muscularity based onhistopathologic scoring. After staining tissue samples to detectαSMA/elastin, 100 pulmonary arterioles, between 10 μm and 50 μm in size,per animal were categorized as non-muscularized, partially muscularized,or completely muscularized. Pulmonary arterioles from vehicle treatedrats were determined to be 62.3% completely muscularized, 36.4%partially muscularized, and 1.4% non-muscularized. Sildenafil treatmenthad only a modest effect on decreasing vessel muscularity (e.g.,pulmonary arterioles being 57.9% completely muscularized, 41.6%partially muscularized, and 0.9% non-muscularized). In contrast,ActRIIA-mFc treatment resulted in significant decreases in vesselmuscularity compared to sildenafil treated animals (e.g., pulmonaryarterioles being 25.8% completely muscularized, 66.9% partiallymuscularized, and 7.3% non-muscularized compared to vehicle treatedanimals). Histopathological scoring of smooth muscle hypertrophy ofpulmonary arterioles were also recorded as follows: 0 (normal), 1(minimal), 2 (mild), 3 (moderate), or 4 (marked). Vehicle treated ratshad an average smooth muscle hypertrophy of moderate to marked (3.8score). Again, sildenafil treatment was observed to have a modest effecton hypertrophy with an average score of 3 (moderate). While ActRIIA-mFctreated animals were observed to have significant reduction in smoothmuscle hypertrophy (average score of 1.6) compared to both vehicle andsildenafil treated animals. Overall, ActRIIA-mFc treatment significantlyreduced vessel muscularity and hypertrophy in this PAH model.

Together, these data demonstrate that both ActRIIA-mFc andALK4-Fc:ActRIIB-Fc are effective in ameliorate various complications ofPAH in this monocrotaline-induced model. In particular, both ActRIIA-mFcand ALK4-Fc:ActRIIB-Fc had a greater effect in reducing artery pressure,right heart hypertrophy, and vascular muscularization than was observedfor sildenafil, which is an approved drug for the treatment of PAH.Furthermore, the data indicate that other GDF/BMP antagonists,particularly ones having activities similar to ActRIIA-mFc andALK4-Fc:ActRIIB-Fc, may be useful in the treatment of PAH, particularlyin preventing or reducing the severity various complications of PAH.

Example 15: Effects of an ActRII Polypeptide and ALK4:ActRIIBHeterodimer on Pulmonary Hypertension in the Sugen Hypoxia Rat Model

The effects of an ActRIIA-mFc fusion protein (ActRIIA-mFc homodimer asdescribed in Example 1 and sildenafil (a phosphodiesterase-5 inhibitorapproved for the treatment of PAH) were further examined the SugenHypoxia model of PAH. In this model, rats receive daily doses ofsemaxanib and are placed in a low oxygen environment (approximately 13%oxygen) to induce PAH 24 hours prior to start of therapy.

Rats were separated into different treatment groups (10 mice pergroup): 1) treatment with semaxanib (200 mg/kg administered s.c. as asingle dose daily)/hypoxia and Tris buffered saline (administered i.p.as 1 ml/kg, every three days) (vehicle treatment group), 2) treatmentwith an ActRIIA-mFc polypeptide (10 mg/kg administered i.p. every threedays) and semaxanib (200 mg/kg administered s.c. as a single dosedaily)/hypoxia, 3) treatment with sildenafil (30 mg/kg administeredorally twice daily) and semaxanib (200 mg/kg administered s.c. as asingle dose daily)/hypoxia, and 4) control rats (Tris buffered salineadministered i.p. as 1 ml/kg, every three days). Rats were treated for28 days. Body weights were recorded prior to first dose on Day 1 andthen weekly throughout the study.

On day 28, rats were anesthetized by an intraperitoneal injection ofketamine/xylazine (80/10 mg/kg). An incision was made in the neck, and ajugular vein was isolated and ligated anteriorly. A fluid-filledpressure catheter was introduced into the right jugular vein to measurepulmonary artery pressure (PAP). Another incision was made in theinguinal region, and femoral artery was isolated and ligated anteriorly.A Millar pressure catheter was introduced into a femoral artery tomeasure systolic arterial pressure, diastolic pressure, and heart rate.Mean arterial pressure and right PAP were monitored using the NotocordHEM (Croissy sur Seine, Frnace) v3.5 data capture system forapproximately 5-10 minutes until stable measurements were obtained.During the measurements, rats were maintained at approximately 37° C. ona heating pad and body temperature was monitored throughout theprocedure with a rectal temperature probe. At the conclusion of theprocedure, rats were euthanized, and the hearts and lungs were removed.The entire heart was weighed. Next, the atria were removed and the leftventricle with septum (LV+S) was separated from the right ventricle(RV). The ventricles were weighed separately. Hypertrophy was assessed,in part, by calculating RV/LV+S. The lungs were also weighed.

Compared to control animals, semaxanib/hypoxia treated rats (vehicletreatment group) were observed to have decreased body weight, elevatedPAP, right heart hypertrophy, and increased lung weight, indicatingestablishment of PAH. Sildenafil treatment reduced mean pulmonaryarterial pressure by 22.4% and decreased right heart hypertrophy by 10%compared to vehicle treated animals. Again, ActRIIA-mFc treatment wasfound have significantly greater effects in treating PAH in this modelcompared to sildenafil. For example, ActRIIA-mFc treatment resulted in areduction of mean pulmonary arterial pressure by 51.3% and decreasedright heart hypertrophy by 53.5% compared to vehicle treated animals.

Similar trends were observed on vessel muscularity based onhistopathologic scoring. After staining tissue samples to detectαSMA/elastin, 100 pulmonary arterioles, between 10 μm and 50 μm in size,per animal were categorized as non-muscularized, partially muscularized,or completely muscularized. Pulmonary arterioles from vehicle treatedrats were determined to be 72.5% completely muscularized, 27.4%partially muscularized, and 0.1% non-muscularized. Sildenafil treatmenthad only a modest effect on decreasing vessel muscularity (e.g.,pulmonary arterioles being 67.4% completely muscularized, 31.6%partially muscularized, and 1.0% non-muscularized) compared to vehicletreated animals. In contrast, ActRIIA-mFc treatment resulted insignificant decreases in vessel muscularity compared to sildenafiltreated animals (e.g., pulmonary arterioles being 29.3% completelymuscularized, 69.3% partially muscularized, and 1.4% non-muscularizedcompared to vehicle treated animals). Histopathological scoring ofsmooth muscle hypertrophy of pulmonary arterioles were also recorded asfollows: 0 (normal), 1 (minimal), 2 (mild), 3 (moderate), or 4 (marked).Vehicle treated rats had an average smooth muscle hypertrophy ofmoderate to marked (3.6 score). Again, sildenafil treatment was observedto have a modest effect on hypertrophy with an average score of 3(moderate). While ActRIIA-mFc treated animals were observed to havesignificant reduction in smooth muscle hypertrophy (average score of1.4) compared to sildenafil treated animals. Overall, ActRIIA-mFctreatment significantly reduced vessel muscularity and hypertrophy inthis PAH model.

Together, these data demonstrate that ActRIIA-mFc is effective inameliorate various complications of PAH in the Sugen Hypoxia model. Inparticular, ActRIIA-mFc had a greater effect in reducing arterypressure, right heart hypertrophy, and vessel muscularization than wasobserved for sildenafil, which is an approved drug for the treatment ofPAH. Furthermore, the data indicate that other GDF/BMP antagonists,particularly ones having activities similar to ActRIIA-mFc may be usefulin the treatment of PAH, particularly in preventing or reducing theseverity various complications of PAH.

INCORPORATION BY REFERENCE

All publications and patents mentioned herein are hereby incorporated byreference in their entirety as if each individual publication or patentwas specifically and individually indicated to be incorporated byreference.

While specific embodiments of the subject matter have been discussed,the above specification is illustrative and not restrictive. Manyvariations will become apparent to those skilled in the art upon reviewof this specification and the claims below. The full scope of theinvention should be determined by reference to the claims, along withtheir full scope of equivalents, and the specification, along with suchvariations.

1. A method of treating pulmonary arterial hypertension, comprisingadministering to a patient in need thereof an effective amount of apolypeptide comprising an amino acid sequence that is at least 70%, 75%,80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99%, or 100% identical to an amino acid sequence that begins at anyone of amino acids 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 of SEQ IDNO: 9 and ends at any one of amino acids 110, 111, 112, 113, 114, 115,116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,130, 131, 132, 133, 134, or 135 of SEQ ID NO:
 9. 2. A method of treatingpulmonary hypertension, comprising administering to a patient in needthereof an effective amount of a GDF/BMP antagonist, wherein the GDF/BMPantagonist is a heteromultimer comprising an ALK4 polypeptide and anActRIIB polypeptide. 3-70. (canceled)
 71. The method of claim 1, whereinthe method comprises administering to the patient a BMP9 polypeptide.72. The method of claim 71, wherein the BMP9 polypeptide is a matureBMP9 polypeptide.
 73. The method of claim 71, wherein the BMP9polypeptide comprises a BMP9 prodomain polypeptide.
 74. The method ofclaim 71, wherein the BMP9 polypeptide is administered in apharmaceutical preparation.
 75. The method of claim 74, wherein thepharmaceutical preparation further comprises a BMP9 prodomainpolypeptide.
 76. The method of claim 75, wherein the BMP9 polypeptide isnoncovalently associated with the BMP9 prodomain polypeptide.
 77. Themethod of claim 74, wherein the pharmaceutical preparation issubstantially free of, or does not comprise, a BMP9 prodomainpolypeptide.
 78. The method of claim 1, wherein the patient has restingpulmonary arterial pressure (PAP) of at least 25 mm Hg (e.g., 25, 30,35, 40, 45, or 50 mm Hg).
 79. The method of claim 1, wherein the methodreduces PAP in the patient.
 80. The method of claim 79, wherein themethod reduces PAP by at least 3 mmHg (e.g., at least 3, 5, 7, 10, 12,15, 20, or 25 mm Hg) in the patient.
 81. The method of claim 1, whereinthe method reduces pulmonary vascular resistance in the patient.
 82. Themethod of claim 1, wherein the method increases pulmonary capillarywedge pressure.
 83. The method of claim 1, wherein the method increasesleft ventricular end-diastolic pressure.
 84. The method of claim 1,wherein the method increases exercise capacity of the patient.
 85. Themethod of claim 84, wherein the method increases the patient's 6-minutewalk distance.
 86. The method of claim 85, wherein the method increasesthe patient's 6-minute walk distance by at least 10 meters (e.g., atleast 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more meters).
 87. Themethod of claim 1, wherein the method reduces the patient's Borg dyspneaindex (BDI).
 88. The method of claim 87, wherein the method reduces thepatient's BDI by at least 0.5 index points (e.g., at least 0.5, 1, 1.5,2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, or 10index points).
 89. The method of claim 1, wherein the patient hasFunctional Class I, Class II, Class III, or Class IV pulmonaryhypertension as recognized by the World Health Organization.
 90. Themethod of claim 89, wherein the method prevents or delays pulmonaryhypertension Functional Class progression (e.g., prevents or delaysprogression from Functional Class I to Class II, Class II to Class III,or Class III to Class IV pulmonary hypertension as recognized by theWorld Health Organization).
 91. The method of claim 89, wherein themethod promotes or increases pulmonary hypertension Functional Classregression (e.g., promotes or increases regression from Class IV toClass III, Class III to Class II, or Class II to Class I pulmonaryhypertension as recognized by the World Health Organization). 92-118.(canceled)
 119. The method of claim 1 or 118, wherein the polypeptide isselected from the group consisting of: a. polypeptide comprising anamino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identicalto the sequence of amino acids corresponding to residues 30-110 of SEQID NO: 9 b. polypeptide comprising an amino acid sequence that is atleast 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequenceSEQ ID NO: 10; and c. polypeptide comprising an amino acid sequence thatis at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acidsequence of SEQ ID NO:
 11. 120. The method of claim 119, wherein thepolypeptide is a fusion protein further comprising an Fc domain of animmunoglobulin.
 121. The method of claim 120, wherein the Fc domain ofthe immunoglobulin is an Fc domain of an IgG1 immunoglobulin. 122-123.(canceled)
 124. The method of claim 1, wherein the polypeptide comprisesan amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identical to the amino acid sequence of SEQ ID NO:
 32. 125. The methodof claim 1, wherein the polypeptide is part of a homodimer proteincomplex.
 126. The method of claim 1, wherein the polypeptide isglycosylated. 127-151. (canceled)
 152. The method of claim 1, whereinthe ActRIIA polypeptides binds to one or more ligands selected from thegroup consisting of: activin A, activin B, and GDF11.
 153. The method ofclaim 152, wherein the ActRIIA polypeptide further binds to one or moreligands selected from the group consisting of: BMP10, GDF8, and BMP6.